PDB Short entry for 3GPP HEADER LYASE/DNA 23-MAR-09 3GPP TITLE MUTM ENCOUNTERING AN INTRAHELICAL 8-OXOGUANINE (OXOG) LESION IN EC3- TITLE 2 T224P COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.2.99.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 GENE: MUTM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA GLYCOSYLASE, DNA REPAIR, DAMAGE SEARCH, BASE EXTRUSION, DISULFIDE KEYWDS 2 CROSSLINKING, DNA DAMAGE, DNA-BINDING, GLYCOSIDASE, HYDROLASE, KEYWDS 3 LYASE, METAL-BINDING, MULTIFUNCTIONAL ENZYME, ZINC-FINGER, LYASE-DNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.C.SPONG,Y.QI,G.L.VERDINE REVDAT 6 06-SEP-23 3GPP 1 REMARK REVDAT 5 20-OCT-21 3GPP 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3GPP 1 REMARK REVDAT 3 13-JUL-11 3GPP 1 VERSN REVDAT 2 02-FEB-10 3GPP 1 JRNL REVDAT 1 10-NOV-09 3GPP 0 JRNL AUTH Y.QI,M.C.SPONG,K.NAM,A.BANERJEE,S.JIRALERSPONG,M.KARPLUS, JRNL AUTH 2 G.L.VERDINE JRNL TITL ENCOUNTER AND EXTRUSION OF AN INTRAHELICAL LESION BY A DNA JRNL TITL 2 REPAIR ENZYME. JRNL REF NATURE V. 462 762 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 20010681 JRNL DOI 10.1038/NATURE08561 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 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) : 31.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 23314 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1119 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) : 1424 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1954 REMARK 3 NUCLEIC ACID ATOMS : 534 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2593 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3622 ; 1.374 ; 2.239 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 249 ; 5.464 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;26.026 ;21.149 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 331 ;15.859 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;18.422 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 9 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 2 A 31 REMARK 3 ORIGIN FOR THE GROUP (A): -22.0890 59.1130 8.9500 REMARK 3 T TENSOR REMARK 3 T11: -0.2771 T22: 0.1179 REMARK 3 T33: -0.0209 T12: -0.0249 REMARK 3 T13: 0.0424 T23: 0.0335 REMARK 3 L TENSOR REMARK 3 L11: 1.4455 L22: 2.5116 REMARK 3 L33: 2.3337 L12: 0.0993 REMARK 3 L13: 0.5572 L23: -0.6690 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: -0.2602 S13: -0.0842 REMARK 3 S21: -0.0373 S22: -0.1064 S23: 0.1897 REMARK 3 S31: 0.1244 S32: -0.2595 S33: 0.0726 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 32 A 41 REMARK 3 ORIGIN FOR THE GROUP (A): -9.2880 70.0110 11.6020 REMARK 3 T TENSOR REMARK 3 T11: -0.1676 T22: 0.1544 REMARK 3 T33: -0.0467 T12: -0.0301 REMARK 3 T13: -0.0421 T23: 0.0349 REMARK 3 L TENSOR REMARK 3 L11: 6.2991 L22: 2.3860 REMARK 3 L33: 6.3901 L12: 2.6015 REMARK 3 L13: -3.0387 L23: -3.7964 REMARK 3 S TENSOR REMARK 3 S11: 0.1942 S12: -0.4194 S13: 0.0916 REMARK 3 S21: 0.3266 S22: -0.4128 S23: -0.4641 REMARK 3 S31: -0.4324 S32: -0.0255 S33: 0.2185 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 42 A 112 REMARK 3 ORIGIN FOR THE GROUP (A): -20.3100 62.6200 9.1330 REMARK 3 T TENSOR REMARK 3 T11: -0.1956 T22: 0.1277 REMARK 3 T33: -0.0349 T12: 0.0133 REMARK 3 T13: -0.0001 T23: 0.0459 REMARK 3 L TENSOR REMARK 3 L11: 0.9567 L22: 1.0300 REMARK 3 L33: 1.1114 L12: -0.4690 REMARK 3 L13: 0.3935 L23: -0.4741 REMARK 3 S TENSOR REMARK 3 S11: -0.0692 S12: -0.1732 S13: -0.0647 REMARK 3 S21: -0.0095 S22: -0.0093 S23: -0.0273 REMARK 3 S31: 0.0398 S32: -0.0506 S33: 0.0785 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 : A 113 A 150 REMARK 3 ORIGIN FOR THE GROUP (A): -5.9600 50.7930 10.0780 REMARK 3 T TENSOR REMARK 3 T11: -0.2166 T22: 0.1817 REMARK 3 T33: -0.0110 T12: 0.1008 REMARK 3 T13: 0.0312 T23: 0.1421 REMARK 3 L TENSOR REMARK 3 L11: 0.6488 L22: 2.6820 REMARK 3 L33: 3.3967 L12: -0.4042 REMARK 3 L13: -0.2518 L23: -2.6745 REMARK 3 S TENSOR REMARK 3 S11: -0.0373 S12: -0.2689 S13: 0.1800 REMARK 3 S21: -0.5784 S22: -0.4271 S23: -0.1715 REMARK 3 S31: 0.2882 S32: 0.5273 S33: 0.4644 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 151 A 199 REMARK 3 ORIGIN FOR THE GROUP (A): -4.9330 39.1390 24.9320 REMARK 3 T TENSOR REMARK 3 T11: -0.2069 T22: 0.1352 REMARK 3 T33: -0.0181 T12: 0.0571 REMARK 3 T13: 0.0447 T23: 0.2201 REMARK 3 L TENSOR REMARK 3 L11: 0.3496 L22: 2.0129 REMARK 3 L33: 3.7625 L12: 0.1164 REMARK 3 L13: -0.0818 L23: -2.5977 REMARK 3 S TENSOR REMARK 3 S11: 0.1635 S12: 0.1612 S13: 0.0346 REMARK 3 S21: 0.0643 S22: -0.5004 S23: -0.1587 REMARK 3 S31: 0.0170 S32: 0.2440 S33: 0.3369 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 200 A 215 REMARK 3 ORIGIN FOR THE GROUP (A): -12.3320 33.9170 19.0770 REMARK 3 T TENSOR REMARK 3 T11: -0.0270 T22: -0.0068 REMARK 3 T33: -0.0724 T12: 0.0442 REMARK 3 T13: 0.0055 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 24.2368 L22: 8.0949 REMARK 3 L33: 9.5413 L12: -8.0097 REMARK 3 L13: 6.2814 L23: -8.6418 REMARK 3 S TENSOR REMARK 3 S11: 0.2533 S12: -0.2151 S13: -0.7022 REMARK 3 S21: -1.1858 S22: -0.0737 S23: 0.2713 REMARK 3 S31: 0.6427 S32: -0.2659 S33: -0.1796 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 : A 216 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): -20.0570 37.3560 33.5300 REMARK 3 T TENSOR REMARK 3 T11: -0.1430 T22: 0.1513 REMARK 3 T33: -0.0502 T12: 0.0910 REMARK 3 T13: 0.0121 T23: 0.1310 REMARK 3 L TENSOR REMARK 3 L11: 4.6834 L22: 9.7781 REMARK 3 L33: 12.1454 L12: 5.6147 REMARK 3 L13: -0.3757 L23: -6.4634 REMARK 3 S TENSOR REMARK 3 S11: 0.1176 S12: 0.4665 S13: 0.2897 REMARK 3 S21: -0.1577 S22: 0.2581 S23: 1.0576 REMARK 3 S31: -0.4312 S32: -0.7765 S33: -0.3757 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 : A 254 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): -10.8460 38.9810 36.5700 REMARK 3 T TENSOR REMARK 3 T11: -0.1035 T22: 0.1122 REMARK 3 T33: -0.0475 T12: -0.0865 REMARK 3 T13: -0.0580 T23: 0.1346 REMARK 3 L TENSOR REMARK 3 L11: 1.3152 L22: 4.2188 REMARK 3 L33: 3.8059 L12: -0.4810 REMARK 3 L13: -0.3414 L23: -3.7518 REMARK 3 S TENSOR REMARK 3 S11: 0.1401 S12: -0.0631 S13: -0.0917 REMARK 3 S21: 0.6315 S22: -0.4081 S23: -0.3069 REMARK 3 S31: -0.4776 S32: 0.3650 S33: 0.2679 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 14 REMARK 3 RESIDUE RANGE : C 3 C 15 REMARK 3 ORIGIN FOR THE GROUP (A): -4.0180 59.3180 29.2590 REMARK 3 T TENSOR REMARK 3 T11: -0.0788 T22: 0.3195 REMARK 3 T33: 0.0330 T12: 0.0562 REMARK 3 T13: -0.2728 T23: 0.0671 REMARK 3 L TENSOR REMARK 3 L11: 12.2960 L22: 8.2233 REMARK 3 L33: 1.7813 L12: -5.1880 REMARK 3 L13: -2.2881 L23: -0.9867 REMARK 3 S TENSOR REMARK 3 S11: -0.8396 S12: -1.7441 S13: 0.6688 REMARK 3 S21: 1.3214 S22: 0.5516 S23: -1.6853 REMARK 3 S31: -0.1776 S32: 0.5073 S33: 0.2881 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3GPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24531 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9880 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) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1R2Y, PROTEIN PART ONLY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, SODIUM CACODYLATE, GLYCEROL, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.62150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.92050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.62150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.92050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 LYS A 217 REMARK 465 GLY A 218 REMARK 465 GLY A 219 REMARK 465 SER A 220 REMARK 465 THR A 221 REMARK 465 VAL A 222 REMARK 465 ARG A 223 REMARK 465 PRO A 224 REMARK 465 TYR A 225 REMARK 465 VAL A 226 REMARK 465 ASN A 227 REMARK 465 THR A 228 REMARK 465 GLN A 229 REMARK 465 GLY A 230 REMARK 465 GLU A 231 REMARK 465 ALA A 232 REMARK 465 GLY A 233 REMARK 465 THR A 234 REMARK 465 PHE A 235 REMARK 465 GLN A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 DA B 1 REMARK 465 DG B 15 REMARK 465 DC B 16 REMARK 465 DT C 1 REMARK 465 DG C 2 REMARK 465 DC C 16 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 38 CG CD NE CZ NH1 NH2 REMARK 470 MET A 77 CG SD CE REMARK 470 GLU A 150 CD OE1 OE2 REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 LYS A 198 CG CD CE NZ REMARK 470 MET A 216 CG SD CE 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 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG C 9 O4' - C1' - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT C 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 14 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 3.6 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 LEU A 66 -150.91 -111.66 REMARK 500 ARG A 76 -138.30 50.05 REMARK 500 ASP A 110 105.02 -160.45 REMARK 500 VAL A 241 -38.79 -133.04 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 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 249 SG REMARK 620 2 CYS A 252 SG 109.9 REMARK 620 3 CYS A 269 SG 112.3 99.2 REMARK 620 4 CYS A 272 SG 107.5 109.4 118.3 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 ZN A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GPU RELATED DB: PDB REMARK 900 RELATED ID: 3GPX RELATED DB: PDB REMARK 900 RELATED ID: 3GPY RELATED DB: PDB REMARK 900 RELATED ID: 3GQ3 RELATED DB: PDB REMARK 900 RELATED ID: 3GQ4 RELATED DB: PDB REMARK 900 RELATED ID: 3GQ5 RELATED DB: PDB DBREF 3GPP A 2 274 UNP P84131 P84131_BACST 2 274 DBREF 3GPP B 1 16 PDB 3GPP 3GPP 1 16 DBREF 3GPP C 1 16 PDB 3GPP 3GPP 1 16 SEQADV 3GPP GLU A 3 UNP P84131 GLN 3 CONFLICT SEQADV 3GPP CYS A 166 UNP P84131 GLN 166 ENGINEERED MUTATION SEQADV 3GPP PRO A 224 UNP P84131 THR 224 ENGINEERED MUTATION SEQRES 1 A 273 PRO GLU LEU PRO GLU VAL GLU THR ILE ARG ARG THR LEU SEQRES 2 A 273 LEU PRO LEU ILE VAL GLY LYS THR ILE GLU ASP VAL ARG SEQRES 3 A 273 ILE PHE TRP PRO ASN ILE ILE ARG HIS PRO ARG ASP SER SEQRES 4 A 273 GLU ALA PHE ALA ALA ARG MET ILE GLY GLN THR VAL ARG SEQRES 5 A 273 GLY LEU GLU ARG ARG GLY LYS PHE LEU LYS PHE LEU LEU SEQRES 6 A 273 ASP ARG ASP ALA LEU ILE SER HIS LEU ARG MET GLU GLY SEQRES 7 A 273 ARG TYR ALA VAL ALA SER ALA LEU GLU PRO LEU GLU PRO SEQRES 8 A 273 HIS THR HIS VAL VAL PHE CYS PHE THR ASP GLY SER GLU SEQRES 9 A 273 LEU ARG TYR ARG ASP VAL ARG LYS PHE GLY THR MET HIS SEQRES 10 A 273 VAL TYR ALA LYS GLU GLU ALA ASP ARG ARG PRO PRO LEU SEQRES 11 A 273 ALA GLU LEU GLY PRO GLU PRO LEU SER PRO ALA PHE SER SEQRES 12 A 273 PRO ALA VAL LEU ALA GLU ARG ALA VAL LYS THR LYS ARG SEQRES 13 A 273 SER VAL LYS ALA LEU LEU LEU ASP CYS THR VAL VAL ALA SEQRES 14 A 273 GLY PHE GLY ASN ILE TYR VAL ASP GLU SER LEU PHE ARG SEQRES 15 A 273 ALA GLY ILE LEU PRO GLY ARG PRO ALA ALA SER LEU SER SEQRES 16 A 273 SER LYS GLU ILE GLU ARG LEU HIS GLU GLU MET VAL ALA SEQRES 17 A 273 THR ILE GLY GLU ALA VAL MET LYS GLY GLY SER THR VAL SEQRES 18 A 273 ARG PRO TYR VAL ASN THR GLN GLY GLU ALA GLY THR PHE SEQRES 19 A 273 GLN HIS HIS LEU TYR VAL TYR GLY ARG GLN GLY ASN PRO SEQRES 20 A 273 CYS LYS ARG CYS GLY THR PRO ILE GLU LYS THR VAL VAL SEQRES 21 A 273 ALA GLY ARG GLY THR HIS TYR CYS PRO ARG CYS GLN ARG SEQRES 1 B 16 DA DG DG DT DA DG DA DT DC DC DG DG DA SEQRES 2 B 16 DC DG DC SEQRES 1 C 16 DT DG DC DG DT DC DC 8OG DG DA DT DC DT SEQRES 2 C 16 DA DC DC MODRES 3GPP 8OG C 8 DG HET 8OG C 8 23 HET ZN A 300 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 8OG C10 H14 N5 O8 P FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *73(H2 O) HELIX 1 1 GLU A 3 VAL A 19 1 17 HELIX 2 2 TRP A 30 ASN A 32 5 3 HELIX 3 3 ASP A 39 ILE A 48 1 10 HELIX 4 4 LYS A 122 ASP A 126 1 5 HELIX 5 5 SER A 144 LYS A 154 1 11 HELIX 6 6 SER A 158 ASP A 165 1 8 HELIX 7 7 GLY A 173 GLY A 185 1 13 HELIX 8 8 PRO A 191 LEU A 195 5 5 HELIX 9 9 SER A 196 MET A 216 1 21 SHEET 1 A 4 ILE A 23 ILE A 28 0 SHEET 2 A 4 THR A 94 PHE A 100 -1 O CYS A 99 N GLU A 24 SHEET 3 A 4 SER A 104 ARG A 109 -1 O TYR A 108 N VAL A 96 SHEET 4 A 4 ARG A 80 SER A 85 -1 N ALA A 82 O ARG A 107 SHEET 1 B 5 ILE A 34 HIS A 36 0 SHEET 2 B 5 THR A 116 ALA A 121 1 O MET A 117 N ARG A 35 SHEET 3 B 5 ASP A 69 HIS A 74 -1 N ILE A 72 O HIS A 118 SHEET 4 B 5 PHE A 61 LEU A 65 -1 N LEU A 62 O SER A 73 SHEET 5 B 5 GLY A 54 ARG A 58 -1 N GLU A 56 O LYS A 63 SHEET 1 C 2 GLU A 257 VAL A 261 0 SHEET 2 C 2 ARG A 264 TYR A 268 -1 O TYR A 268 N GLU A 257 LINK O3' DC C 7 P 8OG C 8 1555 1555 1.60 LINK O3' 8OG C 8 P DG C 9 1555 1555 1.60 LINK SG CYS A 249 ZN ZN A 300 1555 1555 2.41 LINK SG CYS A 252 ZN ZN A 300 1555 1555 2.34 LINK SG CYS A 269 ZN ZN A 300 1555 1555 2.28 LINK SG CYS A 272 ZN ZN A 300 1555 1555 2.22 CISPEP 1 HIS A 36 PRO A 37 0 -6.37 CISPEP 2 PRO A 129 PRO A 130 0 0.94 SITE 1 AC1 4 CYS A 249 CYS A 252 CYS A 269 CYS A 272 CRYST1 45.243 93.841 103.405 90.00 90.00 90.00 P 21 21 21 4 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 0.022103 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009671 0.00000