PDB Short entry for 3IBK HEADER RNA 16-JUL-09 3IBK TITLE CRYSTAL STRUCTURE OF A TELOMERIC RNA QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(5BU)P*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS RNA QUADRUPLEX, BIMOLECULAR QUADRUPLEX, PARALLEL STRANDED, RNA EXPDTA X-RAY DIFFRACTION AUTHOR G.W.COLLIE,S.NEIDLE,G.N.PARKINSON REVDAT 3 19-FEB-14 3IBK 1 JRNL REVDAT 2 13-JUL-11 3IBK 1 VERSN REVDAT 1 12-MAY-10 3IBK 0 JRNL AUTH G.W.COLLIE,S.M.HAIDER,S.NEIDLE,G.N.PARKINSON JRNL TITL A CRYSTALLOGRAPHIC AND MODELLING STUDY OF A HUMAN TELOMERIC JRNL TITL 2 RNA (TERRA) QUADRUPLEX JRNL REF NUCLEIC ACIDS RES. V. 38 5569 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20413582 JRNL DOI 10.1093/NAR/GKQ259 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3899 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 176 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 266 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.1960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 520 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 45 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) : 24.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.25000 REMARK 3 B12 (A**2) : -0.08000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.780 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 497 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 774 ; 0.859 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL 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): 99 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 224 ; 0.023 ; 0.020 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): 497 ; 2.555 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 774 ; 3.630 ; 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 : 4 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 6 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8518 25.7515 38.1223 REMARK 3 T TENSOR REMARK 3 T11: 0.0476 T22: 0.0833 REMARK 3 T33: 0.0552 T12: -0.0084 REMARK 3 T13: -0.0063 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 3.9943 L22: 4.9998 REMARK 3 L33: 4.4407 L12: -2.0726 REMARK 3 L13: 0.3627 L23: -1.3727 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: -0.2550 S13: 0.0783 REMARK 3 S21: 0.6039 S22: 0.1461 S23: 0.3743 REMARK 3 S31: -0.2369 S32: -0.2454 S33: -0.1272 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 7 A 12 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5425 30.1621 33.7897 REMARK 3 T TENSOR REMARK 3 T11: 0.0653 T22: 0.0650 REMARK 3 T33: 0.0645 T12: -0.0005 REMARK 3 T13: -0.0034 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 2.2504 L22: 4.2129 REMARK 3 L33: 1.2188 L12: -0.4003 REMARK 3 L13: -0.3558 L23: 2.2576 REMARK 3 S TENSOR REMARK 3 S11: 0.0477 S12: 0.0641 S13: 0.1474 REMARK 3 S21: -0.3166 S22: 0.0797 S23: -0.1867 REMARK 3 S31: -0.4579 S32: 0.0830 S33: -0.1275 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 : B 14 B 17 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1835 18.4603 28.9260 REMARK 3 T TENSOR REMARK 3 T11: 0.1232 T22: 0.1060 REMARK 3 T33: 0.1106 T12: -0.0003 REMARK 3 T13: 0.0048 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 4.0719 L22: 0.5588 REMARK 3 L33: 1.4492 L12: -1.3718 REMARK 3 L13: 0.3259 L23: -0.4806 REMARK 3 S TENSOR REMARK 3 S11: -0.1696 S12: 0.9455 S13: -0.4775 REMARK 3 S21: -0.6367 S22: 0.2091 S23: 0.0785 REMARK 3 S31: 0.1174 S32: 0.0423 S33: -0.0394 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 18 B 24 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8103 18.1767 33.2025 REMARK 3 T TENSOR REMARK 3 T11: 0.0072 T22: 0.0043 REMARK 3 T33: -0.0057 T12: -0.0134 REMARK 3 T13: 0.0113 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 5.1351 L22: 1.4768 REMARK 3 L33: 5.5143 L12: 1.7282 REMARK 3 L13: 2.5475 L23: -1.0932 REMARK 3 S TENSOR REMARK 3 S11: 0.0803 S12: 0.1620 S13: -0.6099 REMARK 3 S21: -0.2280 S22: -0.0672 S23: 0.3158 REMARK 3 S31: 0.3998 S32: -0.0236 S33: -0.0132 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 U VALUES: RESIDUAL ONLY REMARK 4 REMARK 4 3IBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB054207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD TITAN CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3912 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 49.869 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.540 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.5.0072 REMARK 200 STARTING MODEL: PDB ENTRY 1K8P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, , KCL, NACL, NACACODYLATE, REMARK 280 POLYAMINE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 12.79233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.58467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.58467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 12.79233 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 U B 19 REMARK 475 A B 20 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 U A 12 C5' C4' O4' C3' O3' C2' O2' REMARK 480 U A 12 C1' N1 C2 O2 N3 C4 O4 REMARK 480 U A 12 C5 C6 REMARK 480 U B 18 O5' C5' C4' O4' C3' O3' C2' REMARK 480 U B 18 O2' C1' N1 C2 O2 N3 C4 REMARK 480 U B 18 O4 C5 C6 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 K A 14 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 3 O6 REMARK 620 2 G A 4 O6 82.8 REMARK 620 3 G A 9 O6 74.0 90.2 REMARK 620 4 G A 10 O6 138.9 63.7 82.5 REMARK 620 5 G B 15 O6 120.9 146.2 75.7 83.8 REMARK 620 6 G B 16 O6 148.7 96.4 137.2 63.4 75.6 REMARK 620 7 G B 21 O6 76.0 132.9 122.3 144.5 79.4 82.2 REMARK 620 8 G B 22 O6 90.3 66.2 153.4 96.7 130.8 61.5 72.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 13 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 4 O6 REMARK 620 2 G A 5 O6 67.6 REMARK 620 3 G A 10 O6 66.1 85.1 REMARK 620 4 G A 11 O6 119.4 72.0 67.2 REMARK 620 5 G B 16 O6 106.4 151.5 67.7 89.0 REMARK 620 6 G B 17 O6 161.7 121.3 127.8 78.9 73.4 REMARK 620 7 G B 22 O6 73.7 129.1 108.2 158.7 70.5 89.4 REMARK 620 8 G B 23 O6 93.4 81.3 158.6 122.9 127.2 73.6 69.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 14 DBREF 3IBK A 1 12 PDB 3IBK 3IBK 1 12 DBREF 3IBK B 13 24 PDB 3IBK 3IBK 13 24 SEQRES 1 A 12 5BU A G G G U U A G G G U SEQRES 1 B 12 5BU A G G G U U A G G G U MODRES 3IBK 5BU A 1 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 3IBK 5BU B 13 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE HET 5BU A 1 18 HET 5BU B 13 18 HET K A 13 1 HET K A 14 1 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM K POTASSIUM ION FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 3 K 2(K 1+) FORMUL 5 HOH *45(H2 O) LINK O3' 5BU A 1 P A A 2 1555 1555 1.59 LINK O3' 5BU B 13 P A B 14 1555 1555 1.59 LINK O6 G A 3 K K A 14 1555 1555 2.84 LINK O6 G A 4 K K A 13 1555 1555 2.83 LINK O6 G A 4 K K A 14 1555 1555 2.96 LINK O6 G A 5 K K A 13 1555 1555 2.66 LINK O6 G A 9 K K A 14 1555 1555 2.74 LINK O6 G A 10 K K A 13 1555 1555 2.86 LINK O6 G A 10 K K A 14 1555 1555 2.91 LINK O6 G A 11 K K A 13 1555 1555 2.71 LINK O6 G B 15 K K A 14 1555 1555 2.65 LINK O6 G B 16 K K A 13 1555 1555 2.72 LINK O6 G B 16 K K A 14 1555 1555 3.00 LINK O6 G B 17 K K A 13 1555 1555 2.64 LINK O6 G B 21 K K A 14 1555 1555 2.69 LINK O6 G B 22 K K A 13 1555 1555 2.71 LINK O6 G B 23 K K A 13 1555 1555 2.69 LINK O6 G B 22 K K A 14 1555 1555 3.13 SITE 1 AC1 9 G A 4 G A 5 G A 10 G A 11 SITE 2 AC1 9 K A 14 G B 16 G B 17 G B 22 SITE 3 AC1 9 G B 23 SITE 1 AC2 9 G A 3 G A 4 G A 9 G A 10 SITE 2 AC2 9 K A 13 G B 15 G B 16 G B 21 SITE 3 AC2 9 G B 22 CRYST1 57.583 57.583 38.377 90.00 90.00 120.00 P 31 2 1 12 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 0.017366 0.010026 0.000000 0.00000 SCALE2 0.000000 0.020053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026057 0.00000 HETATM 1 O5' 5BU A 1 6.307 11.985 39.342 1.00 41.14 O HETATM 2 C5' 5BU A 1 5.506 11.358 40.340 1.00 37.88 C HETATM 3 C4' 5BU A 1 5.617 12.093 41.649 1.00 35.67 C HETATM 4 O4' 5BU A 1 6.983 12.479 41.845 1.00 35.54 O HETATM 5 C3' 5BU A 1 4.831 13.381 41.715 1.00 33.90 C HETATM 6 O3' 5BU A 1 3.525 13.113 42.178 1.00 33.80 O HETATM 7 C2' 5BU A 1 5.612 14.208 42.734 1.00 33.89 C HETATM 8 O2' 5BU A 1 5.187 13.967 44.061 1.00 32.79 O HETATM 9 C1' 5BU A 1 7.037 13.701 42.551 1.00 32.63 C HETATM 10 N1 5BU A 1 7.951 14.609 41.817 1.00 26.32 N HETATM 11 C2 5BU A 1 8.166 15.893 42.288 1.00 23.43 C HETATM 12 O2 5BU A 1 7.575 16.368 43.243 1.00 28.08 O HETATM 13 N3 5BU A 1 9.111 16.602 41.602 1.00 19.79 N HETATM 14 C4 5BU A 1 9.859 16.163 40.513 1.00 21.65 C HETATM 15 O4 5BU A 1 10.676 16.919 39.983 1.00 23.37 O HETATM 16 C5 5BU A 1 9.591 14.815 40.091 1.00 16.94 C HETATM 17 C6 5BU A 1 8.678 14.096 40.733 1.00 23.42 C HETATM 18 BR 5BU A 1 10.515 14.115 38.675 1.00 21.79 BR