PDB Short entry for 2BH2 HEADER TRANSFERASE 06-JAN-05 2BH2 TITLE CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN TITLE 2 COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 23S RRNA(M-5-U1939)-METHYLTRANSFERASE, 23S RRNA URACIL-5- COMPND 5 METHYLTRANSFERASE RUMA; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: IRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND COMPND 9 CYS162; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 23S RIBOSOMAL RNA 1932-1968; COMPND 12 CHAIN: C, D; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: 5-FLUORO-U1939 IS METHYLATED AND ITS 6-C IS COVALENTLY COMPND 15 LINKED TO CYS389 OF RUMA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562 KEYWDS IRON-SULFUR CLUSTER, METHYLTRANSFERASE, RNA MODIFICATION, RNA KEYWDS 2 PROCESSING, TRANSFERASE, RUMA, BASE FLIPPING, SAM, OB-FOLD, PROTEIN- KEYWDS 3 RNA COMPLEX, BASE STACKING, SUBSTRATE SELECTIVITY, GENERAL BASE, KEYWDS 4 PRODUCT RELEASE, 4FE-4S, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.T.LEE,S.AGARWALLA,R.M.STROUD REVDAT 3 13-DEC-23 2BH2 1 REMARK LINK REVDAT 2 24-FEB-09 2BH2 1 VERSN REVDAT 1 30-MAR-05 2BH2 0 JRNL AUTH T.T.LEE,S.AGARWALLA,R.M.STROUD JRNL TITL A UNIQUE RNA FOLD IN THE RUMA-RNA-COFACTOR TERNARY COMPLEX JRNL TITL 2 CONTRIBUTES TO SUBSTRATE SELECTIVITY AND ENZYMATIC FUNCTION JRNL REF CELL(CAMBRIDGE,MASS.) V. 120 599 2005 JRNL REFN ISSN 0092-8674 JRNL PMID 15766524 JRNL DOI 10.1016/J.CELL.2004.12.037 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.T.LEE,S.AGARWALLA,R.M.STROUD REMARK 1 TITL CRYSTAL STRUCTURE OF RUMA, AN IRON-SULFUR CLUSTER CONTAINING REMARK 1 TITL 2 E. COLI RIBOSOMAL RNA 5-METHYLURIDINE METHYLTRANSFERASE REMARK 1 REF STRUCTURE V. 12 397 2004 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 15016356 REMARK 1 DOI 10.1016/J.STR.2004.02.009 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 56408 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3990 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6474 REMARK 3 NUCLEIC ACID ATOMS : 1274 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.84000 REMARK 3 B22 (A**2) : 1.43000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.261 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.547 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8108 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 6649 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11280 ; 2.011 ; 2.178 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15585 ; 0.978 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 832 ; 6.937 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1269 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7996 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1290 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1398 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 7962 ; 0.249 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 4604 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 342 ; 0.186 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 16 ; 0.145 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 89 ; 0.302 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.154 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4168 ; 0.865 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6707 ; 1.534 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3940 ; 2.864 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4549 ; 4.280 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 15 A 74 REMARK 3 ORIGIN FOR THE GROUP (A): 99.5072 9.9881 36.7798 REMARK 3 T TENSOR REMARK 3 T11: 0.2786 T22: 0.5350 REMARK 3 T33: 0.1536 T12: 0.1058 REMARK 3 T13: -0.0235 T23: -0.0767 REMARK 3 L TENSOR REMARK 3 L11: 3.7948 L22: 14.9885 REMARK 3 L33: 14.8569 L12: -4.1223 REMARK 3 L13: 4.1435 L23: -10.0873 REMARK 3 S TENSOR REMARK 3 S11: -0.7991 S12: -1.1220 S13: 0.2183 REMARK 3 S21: 1.6548 S22: 0.9749 S23: 0.0161 REMARK 3 S31: -1.1640 S32: -1.3807 S33: -0.1758 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 75 A 93 REMARK 3 RESIDUE RANGE : A 1 A 1 REMARK 3 RESIDUE RANGE : A 125 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 67.6785 14.4080 22.9060 REMARK 3 T TENSOR REMARK 3 T11: 0.1017 T22: 0.0678 REMARK 3 T33: 0.1510 T12: 0.0012 REMARK 3 T13: 0.0109 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 3.3233 L22: 1.7319 REMARK 3 L33: 1.9301 L12: 0.4573 REMARK 3 L13: 0.7403 L23: 0.5966 REMARK 3 S TENSOR REMARK 3 S11: 0.0569 S12: -0.4628 S13: 0.4062 REMARK 3 S21: 0.0785 S22: -0.1142 S23: 0.2880 REMARK 3 S31: -0.2337 S32: -0.2700 S33: 0.0573 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 94 A 124 REMARK 3 RESIDUE RANGE : A 263 A 432 REMARK 3 RESIDUE RANGE : A 500 A 500 REMARK 3 ORIGIN FOR THE GROUP (A): 81.8381 -7.9910 12.1150 REMARK 3 T TENSOR REMARK 3 T11: 0.0470 T22: 0.0225 REMARK 3 T33: 0.0897 T12: 0.0055 REMARK 3 T13: -0.0010 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 3.0081 L22: 1.2542 REMARK 3 L33: 1.4079 L12: 0.7941 REMARK 3 L13: 0.5080 L23: 0.7182 REMARK 3 S TENSOR REMARK 3 S11: 0.0926 S12: 0.0115 S13: -0.3951 REMARK 3 S21: 0.0542 S22: -0.0153 S23: -0.1600 REMARK 3 S31: 0.1568 S32: 0.2332 S33: -0.0772 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 16 B 74 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1465 -35.2332 27.0436 REMARK 3 T TENSOR REMARK 3 T11: 0.3185 T22: 0.2574 REMARK 3 T33: 0.4170 T12: 0.0003 REMARK 3 T13: 0.1058 T23: 0.1040 REMARK 3 L TENSOR REMARK 3 L11: 1.2196 L22: 3.1654 REMARK 3 L33: 24.4443 L12: 1.1955 REMARK 3 L13: -0.1867 L23: -1.9266 REMARK 3 S TENSOR REMARK 3 S11: -0.3374 S12: -0.0745 S13: -0.8449 REMARK 3 S21: 0.1294 S22: -0.4297 S23: -0.3646 REMARK 3 S31: 1.9260 S32: 1.0259 S33: 0.7672 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 75 B 93 REMARK 3 RESIDUE RANGE : B 1 B 1 REMARK 3 RESIDUE RANGE : B 125 B 262 REMARK 3 ORIGIN FOR THE GROUP (A): 44.6634 -21.3282 7.7016 REMARK 3 T TENSOR REMARK 3 T11: 0.0496 T22: 0.0122 REMARK 3 T33: 0.0501 T12: -0.0119 REMARK 3 T13: 0.0141 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 2.7872 L22: 2.4702 REMARK 3 L33: 1.7528 L12: 0.7873 REMARK 3 L13: 0.1658 L23: 0.2373 REMARK 3 S TENSOR REMARK 3 S11: 0.0014 S12: 0.2908 S13: -0.1767 REMARK 3 S21: -0.1703 S22: 0.0508 S23: -0.4138 REMARK 3 S31: 0.0772 S32: 0.1840 S33: -0.0521 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 94 B 124 REMARK 3 RESIDUE RANGE : B 263 B 431 REMARK 3 RESIDUE RANGE : B 500 B 500 REMARK 3 ORIGIN FOR THE GROUP (A): 31.7650 -2.7394 24.9969 REMARK 3 T TENSOR REMARK 3 T11: 0.0514 T22: 0.0775 REMARK 3 T33: 0.0931 T12: -0.0038 REMARK 3 T13: 0.0377 T23: -0.0682 REMARK 3 L TENSOR REMARK 3 L11: 2.4493 L22: 1.9583 REMARK 3 L33: 0.9674 L12: 1.1834 REMARK 3 L13: -0.2985 L23: -0.0654 REMARK 3 S TENSOR REMARK 3 S11: 0.1610 S12: -0.3993 S13: 0.4069 REMARK 3 S21: 0.2143 S22: -0.1687 S23: 0.2583 REMARK 3 S31: -0.1484 S32: -0.1236 S33: 0.0077 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1932 C 1961 REMARK 3 ORIGIN FOR THE GROUP (A): 83.0028 -3.5500 35.5746 REMARK 3 T TENSOR REMARK 3 T11: 0.3807 T22: 0.4431 REMARK 3 T33: 0.0383 T12: -0.0372 REMARK 3 T13: 0.0225 T23: 0.0448 REMARK 3 L TENSOR REMARK 3 L11: 1.6396 L22: 0.4932 REMARK 3 L33: 2.1081 L12: -1.0148 REMARK 3 L13: 2.5101 L23: -1.0977 REMARK 3 S TENSOR REMARK 3 S11: -0.0481 S12: -0.5369 S13: -0.2117 REMARK 3 S21: 0.1536 S22: 0.2320 S23: 0.1263 REMARK 3 S31: 0.1264 S32: -0.2785 S33: -0.1840 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1932 D 1961 REMARK 3 ORIGIN FOR THE GROUP (A): 35.5851 -24.3373 33.5657 REMARK 3 T TENSOR REMARK 3 T11: 0.3658 T22: 0.3769 REMARK 3 T33: 0.0223 T12: -0.0069 REMARK 3 T13: -0.0294 T23: 0.0440 REMARK 3 L TENSOR REMARK 3 L11: 0.6696 L22: 0.7463 REMARK 3 L33: 2.0258 L12: 0.0492 REMARK 3 L13: -0.4517 L23: 0.7324 REMARK 3 S TENSOR REMARK 3 S11: -0.1027 S12: -0.7633 S13: -0.0204 REMARK 3 S21: 0.3929 S22: 0.0531 S23: -0.0584 REMARK 3 S31: 0.4995 S32: 0.1088 S33: 0.0496 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2BH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1290022217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59411 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1UWV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RUMA-RNA-SAH COMPLEX WAS CRYSTALLIZED REMARK 280 FROM 100 MM SODIUM CACODYLATE, PH 6.5, 1.5 M AMMONIUM SULFATE, REMARK 280 AND 10 MM MGCL2, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 95.03050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.77100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 95.03050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.77100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 S-ADENOSYL-L-METHIONINE => S-ADENOSYL-L-HOMOCYSTEINE REMARK 400 + RRNA + RRNA CONTAINING THYMINE. REMARK 400 CATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION REMARK 400 1939 (M-5-U1939) IN 23S RRNA. REMARK 400 BELONGS TO THE RNA M5U METHYLTRANSFERASE FAMILY. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 PHE A 4 REMARK 465 TYR A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 8 REMARK 465 ARG A 9 REMARK 465 ARG A 10 REMARK 465 THR A 11 REMARK 465 THR A 12 REMARK 465 THR A 13 REMARK 465 ARG A 14 REMARK 465 LYS A 433 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 PHE B 4 REMARK 465 TYR B 5 REMARK 465 SER B 6 REMARK 465 ALA B 7 REMARK 465 LYS B 8 REMARK 465 ARG B 9 REMARK 465 ARG B 10 REMARK 465 THR B 11 REMARK 465 THR B 12 REMARK 465 THR B 13 REMARK 465 ARG B 14 REMARK 465 GLN B 15 REMARK 465 VAL B 432 REMARK 465 LYS B 433 REMARK 465 C C 1962 REMARK 465 U C 1963 REMARK 465 G C 1964 REMARK 465 C C 1965 REMARK 465 A C 1966 REMARK 465 C C 1967 REMARK 465 G C 1968 REMARK 465 C D 1962 REMARK 465 U D 1963 REMARK 465 G D 1964 REMARK 465 C D 1965 REMARK 465 A D 1966 REMARK 465 C D 1967 REMARK 465 G D 1968 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N6 A C 1937 O HOH C 2003 2.01 REMARK 500 OD1 ASP A 292 O HOH A 2090 2.04 REMARK 500 O HOH A 2103 O HOH A 2136 2.17 REMARK 500 O LEU A 138 O THR A 141 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 268 CA ALA A 268 CB 0.127 REMARK 500 MET A 373 SD MET A 373 CE -0.372 REMARK 500 MET B 297 SD MET B 297 CE -0.523 REMARK 500 LYS B 359 CE LYS B 359 NZ -0.154 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 23 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 25 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 115 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 221 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 262 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 358 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 LEU A 362 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 ASP A 363 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP B 115 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 122 CB - CG - OD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG B 132 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 LEU B 228 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 ASP B 358 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 363 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 G C1933 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 A C1937 N9 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 C C1942 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 C C1942 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 U C1946 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 G C1949 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 G C1949 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 U C1951 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 U C1955 C5' - C4' - C3' ANGL. DEV. = 13.6 DEGREES REMARK 500 U C1955 C4' - C3' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 U C1955 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 U C1955 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 U C1956 N1 - C1' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 U C1956 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 U C1956 N3 - C4 - O4 ANGL. DEV. = 4.9 DEGREES REMARK 500 U C1956 C5 - C4 - O4 ANGL. DEV. = -4.1 DEGREES REMARK 500 U C1956 C2 - N1 - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 C C1957 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 A D1932 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 A D1937 O5' - P - OP1 ANGL. DEV. = -6.2 DEGREES REMARK 500 A D1937 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES REMARK 500 A D1937 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 A D1937 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 U D1943 N1 - C1' - C2' ANGL. DEV. = 9.4 DEGREES REMARK 500 U D1943 C3' - O3' - P ANGL. DEV. = -8.3 DEGREES REMARK 500 U D1944 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 G D1949 C5 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 A D1952 C2' - C3' - O3' ANGL. DEV. = 17.9 DEGREES REMARK 500 A D1952 C3' - O3' - P ANGL. DEV. = 12.5 DEGREES REMARK 500 G D1954 C6 - N1 - C2 ANGL. DEV. = -4.0 DEGREES REMARK 500 U D1955 N1 - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 U D1955 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 U D1956 O4' - C1' - N1 ANGL. DEV. = 9.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 86 -58.05 -126.02 REMARK 500 GLN A 92 47.39 -148.44 REMARK 500 ASP A 122 -136.13 -139.25 REMARK 500 ASN A 252 33.80 71.78 REMARK 500 ASP A 346 101.04 -58.63 REMARK 500 HIS A 419 -1.52 70.58 REMARK 500 ASN B 35 43.67 38.89 REMARK 500 VAL B 86 -64.58 -128.79 REMARK 500 GLN B 92 46.67 -140.31 REMARK 500 ASP B 122 -145.05 -151.82 REMARK 500 LYS B 140 -78.52 -53.19 REMARK 500 THR B 141 -178.04 -63.90 REMARK 500 SER B 251 87.57 -152.16 REMARK 500 ASN B 252 -125.38 56.63 REMARK 500 HIS B 419 -7.67 75.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 81 SG REMARK 620 2 SF4 A 501 S1 109.9 REMARK 620 3 SF4 A 501 S2 104.4 108.2 REMARK 620 4 SF4 A 501 S3 124.4 104.5 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 87 SG REMARK 620 2 SF4 A 501 S2 118.2 REMARK 620 3 SF4 A 501 S3 108.1 106.3 REMARK 620 4 SF4 A 501 S4 112.3 106.4 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 SF4 A 501 S1 113.5 REMARK 620 3 SF4 A 501 S3 113.7 106.7 REMARK 620 4 SF4 A 501 S4 114.5 105.8 101.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 162 SG REMARK 620 2 SF4 A 501 S1 103.4 REMARK 620 3 SF4 A 501 S2 111.4 108.7 REMARK 620 4 SF4 A 501 S4 118.4 108.6 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 81 SG REMARK 620 2 SF4 B 501 S1 110.4 REMARK 620 3 SF4 B 501 S2 123.0 105.0 REMARK 620 4 SF4 B 501 S3 103.0 109.7 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 87 SG REMARK 620 2 SF4 B 501 S2 105.3 REMARK 620 3 SF4 B 501 S3 115.9 105.1 REMARK 620 4 SF4 B 501 S4 117.9 107.8 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 90 SG REMARK 620 2 SF4 B 501 S1 113.6 REMARK 620 3 SF4 B 501 S2 112.6 102.8 REMARK 620 4 SF4 B 501 S4 114.4 104.7 107.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 162 SG REMARK 620 2 SF4 B 501 S1 108.9 REMARK 620 3 SF4 B 501 S3 115.1 107.0 REMARK 620 4 SF4 B 501 S4 112.1 105.4 107.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UWV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RUMA, THE IRON-SULFUR CLUSTER CONTAINING E. REMARK 900 COLI 23S RIBOSOMAL RNA 5-METHYLURIDINE METHYLTRANSFERASE DBREF 2BH2 A 1 1 PDB 2BH2 2BH2 1 1 DBREF 2BH2 A 2 433 UNP P55135 RUMA_ECOLI 1 432 DBREF 2BH2 B 1 1 PDB 2BH2 2BH2 1 1 DBREF 2BH2 B 2 433 UNP P55135 RUMA_ECOLI 1 432 DBREF 2BH2 C 1932 1968 PDB 2BH2 2BH2 1932 1968 DBREF 2BH2 D 1932 1968 PDB 2BH2 2BH2 1932 1968 SEQRES 1 A 433 MET ALA GLN PHE TYR SER ALA LYS ARG ARG THR THR THR SEQRES 2 A 433 ARG GLN ILE ILE THR VAL SER VAL ASN ASP LEU ASP SER SEQRES 3 A 433 PHE GLY GLN GLY VAL ALA ARG HIS ASN GLY LYS THR LEU SEQRES 4 A 433 PHE ILE PRO GLY LEU LEU PRO GLN GLU ASN ALA GLU VAL SEQRES 5 A 433 THR VAL THR GLU ASP LYS LYS GLN TYR ALA ARG ALA LYS SEQRES 6 A 433 VAL VAL ARG ARG LEU SER ASP SER PRO GLU ARG GLU THR SEQRES 7 A 433 PRO ARG CYS PRO HIS PHE GLY VAL CYS GLY GLY CYS GLN SEQRES 8 A 433 GLN GLN HIS ALA SER VAL ASP LEU GLN GLN ARG SER LYS SEQRES 9 A 433 SER ALA ALA LEU ALA ARG LEU MET LYS HIS ASP VAL SER SEQRES 10 A 433 GLU VAL ILE ALA ASP VAL PRO TRP GLY TYR ARG ARG ARG SEQRES 11 A 433 ALA ARG LEU SER LEU ASN TYR LEU PRO LYS THR GLN GLN SEQRES 12 A 433 LEU GLN MET GLY PHE ARG LYS ALA GLY SER SER ASP ILE SEQRES 13 A 433 VAL ASP VAL LYS GLN CYS PRO ILE LEU ALA PRO GLN LEU SEQRES 14 A 433 GLU ALA LEU LEU PRO LYS VAL ARG ALA CYS LEU GLY SER SEQRES 15 A 433 LEU GLN ALA MET ARG HIS LEU GLY HIS VAL GLU LEU VAL SEQRES 16 A 433 GLN ALA THR SER GLY THR LEU MET ILE LEU ARG HIS THR SEQRES 17 A 433 ALA PRO LEU SER SER ALA ASP ARG GLU LYS LEU GLU ARG SEQRES 18 A 433 PHE SER HIS SER GLU GLY LEU ASP LEU TYR LEU ALA PRO SEQRES 19 A 433 ASP SER GLU ILE LEU GLU THR VAL SER GLY GLU MET PRO SEQRES 20 A 433 TRP TYR ASP SER ASN GLY LEU ARG LEU THR PHE SER PRO SEQRES 21 A 433 ARG ASP PHE ILE GLN VAL ASN ALA GLY VAL ASN GLN LYS SEQRES 22 A 433 MET VAL ALA ARG ALA LEU GLU TRP LEU ASP VAL GLN PRO SEQRES 23 A 433 GLU ASP ARG VAL LEU ASP LEU PHE CYS GLY MET GLY ASN SEQRES 24 A 433 PHE THR LEU PRO LEU ALA THR GLN ALA ALA SER VAL VAL SEQRES 25 A 433 GLY VAL GLU GLY VAL PRO ALA LEU VAL GLU LYS GLY GLN SEQRES 26 A 433 GLN ASN ALA ARG LEU ASN GLY LEU GLN ASN VAL THR PHE SEQRES 27 A 433 TYR HIS GLU ASN LEU GLU GLU ASP VAL THR LYS GLN PRO SEQRES 28 A 433 TRP ALA LYS ASN GLY PHE ASP LYS VAL LEU LEU ASP PRO SEQRES 29 A 433 ALA ARG ALA GLY ALA ALA GLY VAL MET GLN GLN ILE ILE SEQRES 30 A 433 LYS LEU GLU PRO ILE ARG ILE VAL TYR VAL SER CYS ASN SEQRES 31 A 433 PRO ALA THR LEU ALA ARG ASP SER GLU ALA LEU LEU LYS SEQRES 32 A 433 ALA GLY TYR THR ILE ALA ARG LEU ALA MET LEU ASP MET SEQRES 33 A 433 PHE PRO HIS THR GLY HIS LEU GLU SER MET VAL LEU PHE SEQRES 34 A 433 SER ARG VAL LYS SEQRES 1 B 433 MET ALA GLN PHE TYR SER ALA LYS ARG ARG THR THR THR SEQRES 2 B 433 ARG GLN ILE ILE THR VAL SER VAL ASN ASP LEU ASP SER SEQRES 3 B 433 PHE GLY GLN GLY VAL ALA ARG HIS ASN GLY LYS THR LEU SEQRES 4 B 433 PHE ILE PRO GLY LEU LEU PRO GLN GLU ASN ALA GLU VAL SEQRES 5 B 433 THR VAL THR GLU ASP LYS LYS GLN TYR ALA ARG ALA LYS SEQRES 6 B 433 VAL VAL ARG ARG LEU SER ASP SER PRO GLU ARG GLU THR SEQRES 7 B 433 PRO ARG CYS PRO HIS PHE GLY VAL CYS GLY GLY CYS GLN SEQRES 8 B 433 GLN GLN HIS ALA SER VAL ASP LEU GLN GLN ARG SER LYS SEQRES 9 B 433 SER ALA ALA LEU ALA ARG LEU MET LYS HIS ASP VAL SER SEQRES 10 B 433 GLU VAL ILE ALA ASP VAL PRO TRP GLY TYR ARG ARG ARG SEQRES 11 B 433 ALA ARG LEU SER LEU ASN TYR LEU PRO LYS THR GLN GLN SEQRES 12 B 433 LEU GLN MET GLY PHE ARG LYS ALA GLY SER SER ASP ILE SEQRES 13 B 433 VAL ASP VAL LYS GLN CYS PRO ILE LEU ALA PRO GLN LEU SEQRES 14 B 433 GLU ALA LEU LEU PRO LYS VAL ARG ALA CYS LEU GLY SER SEQRES 15 B 433 LEU GLN ALA MET ARG HIS LEU GLY HIS VAL GLU LEU VAL SEQRES 16 B 433 GLN ALA THR SER GLY THR LEU MET ILE LEU ARG HIS THR SEQRES 17 B 433 ALA PRO LEU SER SER ALA ASP ARG GLU LYS LEU GLU ARG SEQRES 18 B 433 PHE SER HIS SER GLU GLY LEU ASP LEU TYR LEU ALA PRO SEQRES 19 B 433 ASP SER GLU ILE LEU GLU THR VAL SER GLY GLU MET PRO SEQRES 20 B 433 TRP TYR ASP SER ASN GLY LEU ARG LEU THR PHE SER PRO SEQRES 21 B 433 ARG ASP PHE ILE GLN VAL ASN ALA GLY VAL ASN GLN LYS SEQRES 22 B 433 MET VAL ALA ARG ALA LEU GLU TRP LEU ASP VAL GLN PRO SEQRES 23 B 433 GLU ASP ARG VAL LEU ASP LEU PHE CYS GLY MET GLY ASN SEQRES 24 B 433 PHE THR LEU PRO LEU ALA THR GLN ALA ALA SER VAL VAL SEQRES 25 B 433 GLY VAL GLU GLY VAL PRO ALA LEU VAL GLU LYS GLY GLN SEQRES 26 B 433 GLN ASN ALA ARG LEU ASN GLY LEU GLN ASN VAL THR PHE SEQRES 27 B 433 TYR HIS GLU ASN LEU GLU GLU ASP VAL THR LYS GLN PRO SEQRES 28 B 433 TRP ALA LYS ASN GLY PHE ASP LYS VAL LEU LEU ASP PRO SEQRES 29 B 433 ALA ARG ALA GLY ALA ALA GLY VAL MET GLN GLN ILE ILE SEQRES 30 B 433 LYS LEU GLU PRO ILE ARG ILE VAL TYR VAL SER CYS ASN SEQRES 31 B 433 PRO ALA THR LEU ALA ARG ASP SER GLU ALA LEU LEU LYS SEQRES 32 B 433 ALA GLY TYR THR ILE ALA ARG LEU ALA MET LEU ASP MET SEQRES 33 B 433 PHE PRO HIS THR GLY HIS LEU GLU SER MET VAL LEU PHE SEQRES 34 B 433 SER ARG VAL LYS SEQRES 1 C 37 A G C G A A A FMU U C C U U SEQRES 2 C 37 G U C G G G U A A G U U C SEQRES 3 C 37 C G A C C U G C A C G SEQRES 1 D 37 A G C G A A A FMU U C C U U SEQRES 2 D 37 G U C G G G U A A G U U C SEQRES 3 D 37 C G A C C U G C A C G HET FMU C1939 22 HET FMU D1939 22 HET SAH A 500 26 HET SF4 A 501 8 HET SAH B 500 26 HET SF4 B 501 8 HETNAM FMU 5-FLUORO-5-METHYLURIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 3 FMU 2(C10 H16 F N2 O9 P) FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 6 SF4 2(FE4 S4) FORMUL 9 HOH *340(H2 O) HELIX 1 1 SER A 96 LYS A 113 1 18 HELIX 2 2 ALA A 166 SER A 182 1 17 HELIX 3 3 LEU A 183 ARG A 187 5 5 HELIX 4 4 SER A 212 GLU A 226 1 15 HELIX 5 5 ASN A 267 ASP A 283 1 17 HELIX 6 6 PHE A 300 THR A 306 1 7 HELIX 7 7 VAL A 317 ASN A 331 1 15 HELIX 8 8 ASP A 346 GLN A 350 5 5 HELIX 9 9 GLN A 350 ASN A 355 5 6 HELIX 10 10 VAL A 372 LEU A 379 1 8 HELIX 11 11 ASN A 390 ALA A 404 1 15 HELIX 12 12 SER B 96 LYS B 113 1 18 HELIX 13 13 ALA B 166 GLY B 181 1 16 HELIX 14 14 SER B 182 ARG B 187 5 6 HELIX 15 15 SER B 212 GLU B 226 1 15 HELIX 16 16 ASN B 267 ASP B 283 1 17 HELIX 17 17 PHE B 300 THR B 306 1 7 HELIX 18 18 VAL B 317 ASN B 331 1 15 HELIX 19 19 ASP B 346 GLN B 350 5 5 HELIX 20 20 GLN B 350 LYS B 354 5 5 HELIX 21 21 ALA B 369 GLY B 371 5 3 HELIX 22 22 VAL B 372 GLU B 380 1 9 HELIX 23 23 ASN B 390 LYS B 403 1 14 SHEET 1 AA 6 ILE A 16 VAL A 21 0 SHEET 2 AA 6 GLU A 48 VAL A 54 -1 O GLU A 48 N VAL A 21 SHEET 3 AA 6 TYR A 61 ARG A 69 -1 O LYS A 65 N THR A 53 SHEET 4 AA 6 LYS A 37 ILE A 41 1 O THR A 38 N ALA A 62 SHEET 5 AA 6 GLY A 30 HIS A 34 -1 O GLY A 30 N ILE A 41 SHEET 6 AA 6 ASP A 23 LEU A 24 -1 O ASP A 23 N VAL A 31 SHEET 1 AB 8 GLU A 118 ILE A 120 0 SHEET 2 AB 8 TYR A 406 LEU A 414 1 O MET A 413 N ILE A 120 SHEET 3 AB 8 GLU A 424 ARG A 431 -1 O GLU A 424 N LEU A 414 SHEET 4 AB 8 ARG A 383 SER A 388 -1 O ILE A 384 N PHE A 429 SHEET 5 AB 8 LYS A 359 LEU A 362 1 O VAL A 360 N VAL A 385 SHEET 6 AB 8 ARG A 289 LEU A 293 1 O LEU A 291 N LEU A 361 SHEET 7 AB 8 SER A 310 GLU A 315 1 O SER A 310 N VAL A 290 SHEET 8 AB 8 VAL A 336 HIS A 340 1 O THR A 337 N GLY A 313 SHEET 1 AC 7 ILE A 156 ASP A 158 0 SHEET 2 AC 7 GLN A 143 ARG A 149 -1 O PHE A 148 N VAL A 157 SHEET 3 AC 7 ARG A 130 LEU A 138 -1 O SER A 134 N GLY A 147 SHEET 4 AC 7 LEU A 189 ALA A 197 -1 O GLY A 190 N LEU A 135 SHEET 5 AC 7 GLY A 200 HIS A 207 -1 O GLY A 200 N ALA A 197 SHEET 6 AC 7 LEU A 228 ALA A 233 1 O ASP A 229 N MET A 203 SHEET 7 AC 7 GLU A 240 THR A 241 -1 O GLU A 240 N LEU A 232 SHEET 1 AD 2 TRP A 248 SER A 251 0 SHEET 2 AD 2 LEU A 254 THR A 257 -1 O LEU A 254 N SER A 251 SHEET 1 BA 6 ILE B 17 SER B 20 0 SHEET 2 BA 6 ASN B 49 ASP B 57 -1 O ALA B 50 N VAL B 19 SHEET 3 BA 6 TYR B 61 ARG B 69 -1 O ARG B 63 N THR B 55 SHEET 4 BA 6 LYS B 37 ILE B 41 1 O THR B 38 N ALA B 62 SHEET 5 BA 6 GLY B 30 HIS B 34 -1 O GLY B 30 N ILE B 41 SHEET 6 BA 6 ASP B 23 LEU B 24 -1 O ASP B 23 N VAL B 31 SHEET 1 BB 8 GLU B 118 ILE B 120 0 SHEET 2 BB 8 THR B 407 LEU B 414 1 O MET B 413 N ILE B 120 SHEET 3 BB 8 GLU B 424 SER B 430 -1 O GLU B 424 N LEU B 414 SHEET 4 BB 8 ARG B 383 SER B 388 -1 O ILE B 384 N PHE B 429 SHEET 5 BB 8 LYS B 359 LEU B 362 1 O VAL B 360 N VAL B 385 SHEET 6 BB 8 ARG B 289 LEU B 293 1 O LEU B 291 N LEU B 361 SHEET 7 BB 8 SER B 310 GLU B 315 1 O SER B 310 N VAL B 290 SHEET 8 BB 8 VAL B 336 HIS B 340 1 O THR B 337 N GLY B 313 SHEET 1 BC 7 ILE B 156 ASP B 158 0 SHEET 2 BC 7 LEU B 144 ARG B 149 -1 O PHE B 148 N VAL B 157 SHEET 3 BC 7 ARG B 130 TYR B 137 -1 O SER B 134 N GLY B 147 SHEET 4 BC 7 LEU B 189 ALA B 197 -1 O GLY B 190 N LEU B 135 SHEET 5 BC 7 GLY B 200 HIS B 207 -1 O GLY B 200 N ALA B 197 SHEET 6 BC 7 ASP B 229 ASP B 235 1 O ASP B 229 N MET B 203 SHEET 7 BC 7 ILE B 238 SER B 243 -1 O ILE B 238 N ASP B 235 SHEET 1 BD 2 TRP B 248 SER B 251 0 SHEET 2 BD 2 LEU B 254 THR B 257 -1 O LEU B 254 N SER B 251 LINK SG CYS A 389 C6 FMU C1939 1555 1555 1.85 LINK SG CYS B 389 C6 FMU D1939 1555 1555 1.89 LINK O3' A C1938 P FMU C1939 1555 1555 1.59 LINK O3' FMU C1939 P U C1940 1555 1555 1.59 LINK O3' A D1938 P FMU D1939 1555 1555 1.57 LINK O3' FMU D1939 P U D1940 1555 1555 1.62 LINK SG CYS A 81 FE4 SF4 A 501 1555 1555 2.26 LINK SG CYS A 87 FE1 SF4 A 501 1555 1555 2.28 LINK SG CYS A 90 FE2 SF4 A 501 1555 1555 2.33 LINK SG CYS A 162 FE3 SF4 A 501 1555 1555 2.31 LINK SG CYS B 81 FE4 SF4 B 501 1555 1555 2.28 LINK SG CYS B 87 FE1 SF4 B 501 1555 1555 2.32 LINK SG CYS B 90 FE3 SF4 B 501 1555 1555 2.32 LINK SG CYS B 162 FE2 SF4 B 501 1555 1555 2.30 SITE 1 AC1 21 PHE A 263 GLN A 265 PHE A 294 CYS A 295 SITE 2 AC1 21 ASN A 299 PHE A 300 GLU A 315 GLY A 316 SITE 3 AC1 21 VAL A 317 LEU A 320 GLU A 341 ASN A 342 SITE 4 AC1 21 LEU A 343 GLU A 344 ASP A 363 HOH A2112 SITE 5 AC1 21 HOH A2133 HOH A2134 HOH A2135 A C1937 SITE 6 AC1 21 FMU C1939 SITE 1 AC2 9 CYS A 81 CYS A 87 CYS A 90 GLN A 93 SITE 2 AC2 9 GLN A 161 CYS A 162 PRO A 163 ILE A 164 SITE 3 AC2 9 U C1940 SITE 1 AC3 20 PHE B 263 GLN B 265 PHE B 294 CYS B 295 SITE 2 AC3 20 MET B 297 ASN B 299 GLU B 315 GLY B 316 SITE 3 AC3 20 VAL B 317 LEU B 320 GLU B 341 ASN B 342 SITE 4 AC3 20 LEU B 343 ASP B 363 HOH B2088 HOH B2129 SITE 5 AC3 20 HOH B2130 HOH B2131 A D1937 FMU D1939 SITE 1 AC4 7 CYS B 81 CYS B 87 CYS B 90 GLN B 93 SITE 2 AC4 7 GLN B 161 CYS B 162 PRO B 163 CRYST1 190.061 63.542 112.019 90.00 125.15 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.005261 0.000000 0.003705 0.00000 SCALE2 0.000000 0.015738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010918 0.00000