PDB Short entry for 2OZM HEADER TRANSFERASE/DNA 26-FEB-07 2OZM TITLE CRYSTAL STRUCTURE OF RB69 GP43 IN COMPLEX WITH DNA WITH 5-NITP TITLE 2 OPPOSITE AN ABASIC SITE ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEMPLATE DNA; COMPND 3 CHAIN: T; COMPND 4 SYNONYM: GP43; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PRIMER DNA; COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA POLYMERASE; COMPND 12 CHAIN: A; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE RB69; SOURCE 7 ORGANISM_TAXID: 12353; SOURCE 8 GENE: 43; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DNA POLYMERASE, ABASIC SITE, DNA LESION, 5-NITP, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.E.ZAHN,H.BELRHALI,S.S.WALLACE,S.DOUBLIE REVDAT 5 30-AUG-23 2OZM 1 REMARK REVDAT 4 20-OCT-21 2OZM 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK REVDAT 3 18-OCT-17 2OZM 1 REMARK REVDAT 2 24-FEB-09 2OZM 1 VERSN REVDAT 1 23-OCT-07 2OZM 0 JRNL AUTH K.E.ZAHN,H.BELRHAIL,S.S.WALLACE,S.DOUBLIE JRNL TITL CAUGHT BENDING THE A-RULE: CRYSTAL STRUCTURES OF TRANSLESION JRNL TITL 2 DNA SYNTHESIS WITH A NON-NATURAL NUCLEOTIDE JRNL REF BIOCHEMISTRY V. 46 10551 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17718515 JRNL DOI 10.1021/BI7008807 REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0011 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) : 2.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 26082 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2704 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) : 2.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1371 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7328 REMARK 3 NUCLEIC ACID ATOMS : 641 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.91000 REMARK 3 B22 (A**2) : -1.54000 REMARK 3 B33 (A**2) : 3.45000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.449 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.355 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.878 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8261 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11319 ; 1.072 ; 2.062 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 902 ; 4.935 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 372 ;37.698 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1309 ;16.871 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;17.419 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1203 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6109 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3702 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5627 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 412 ; 0.142 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.158 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 48 ; 0.185 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.102 ; 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): 4617 ; 0.458 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7294 ; 0.831 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4406 ; 0.870 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4023 ; 1.539 ; 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 : NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000041782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28816 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.860 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 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: 1IG9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000,SODIUM ACETATE, MAGNESIUM REMARK 280 ACETATE, BETA-MERCAPTOETHANOL, TRIS 7.5, GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.5 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 40.61600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.07100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.74600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.07100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.61600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.74600 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 APPLY THE FOLLOWING TO CHAINS: T, P, A 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 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 25 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 GLU A 254 CG CD OE1 OE2 REMARK 470 LYS A 527 CG CD CE NZ REMARK 470 LYS A 529 CG CD CE NZ REMARK 470 LYS A 532 CG CD CE NZ REMARK 470 LYS A 600 CG CD CE NZ REMARK 470 LYS A 653 CG CD CE NZ REMARK 470 LYS A 696 CG CD CE NZ REMARK 470 LYS A 816 CG CD CE NZ REMARK 470 LYS A 893 CG CD CE NZ 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 O HOH T 45 O HOH P 46 2.15 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 DC T 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT T 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA T 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA T 12 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC T 14 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC T 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG T 16 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC T 17 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG P 1 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DC P 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG P 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA P 13 O4' - C1' - N9 ANGL. DEV. = 2.1 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 TYR A 97 69.07 -112.08 REMARK 500 PHE A 221 -73.12 -133.68 REMARK 500 LYS A 240 -8.86 -56.02 REMARK 500 TYR A 257 -79.67 -107.77 REMARK 500 ASN A 402 -176.75 -177.16 REMARK 500 SER A 414 70.10 40.30 REMARK 500 VAL A 453 -36.81 -131.09 REMARK 500 PRO A 458 12.01 -67.02 REMARK 500 ASN A 505 88.39 177.59 REMARK 500 ASP A 511 -135.72 -140.16 REMARK 500 THR A 622 -63.94 68.19 REMARK 500 ASP A 623 13.91 -142.89 REMARK 500 LYS A 640 10.94 -159.51 REMARK 500 ARG A 658 -53.64 -122.45 REMARK 500 GLU A 686 -86.60 -100.54 REMARK 500 VAL A 793 65.84 34.43 REMARK 500 LEU A 889 -169.05 -119.31 REMARK 500 TYR A 891 -4.63 55.78 REMARK 500 GLU A 892 -113.19 -125.44 REMARK 500 LYS A 893 104.60 170.47 REMARK 500 ALA A 895 86.21 -60.75 REMARK 500 LEU A 897 9.72 50.75 REMARK 500 PHE A 901 58.30 -90.88 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 MG A 904 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 411 OD1 REMARK 620 2 LEU A 412 O 91.7 REMARK 620 3 ASP A 623 OD2 70.3 85.4 REMARK 620 4 N5P A 905 O2A 80.1 153.5 68.1 REMARK 620 5 N5P A 905 O2G 95.9 98.8 165.8 107.0 REMARK 620 6 N5P A 905 O2B 154.9 94.6 86.1 83.5 107.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N5P A 905 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IG9 RELATED DB: PDB REMARK 900 RELATED ID: 1RV2 RELATED DB: PDB REMARK 900 RELATED ID: 2OZS RELATED DB: PDB REMARK 900 RELATED ID: 2OYQ RELATED DB: PDB REMARK 900 RELATED ID: 2P5G RELATED DB: PDB DBREF 2OZM T 1 18 PDB 2OZM 2OZM 1 18 DBREF 2OZM P 1 14 PDB 2OZM 2OZM 1 14 DBREF 2OZM A 1 903 UNP Q38087 DPOL_BPR69 1 903 SEQADV 2OZM ALA A 222 UNP Q38087 ASP 222 ENGINEERED MUTATION SEQADV 2OZM ALA A 327 UNP Q38087 ASP 327 ENGINEERED MUTATION SEQRES 1 T 18 DC DG 3DR DC DT DT DA DT DG DA DC DA DG SEQRES 2 T 18 DC DC DG DC DG SEQRES 1 P 14 DG DC DG DG DC DT DG DT DC DA DT DA DA SEQRES 2 P 14 DDG SEQRES 1 A 903 MET LYS GLU PHE TYR LEU THR VAL GLU GLN ILE GLY ASP SEQRES 2 A 903 SER ILE PHE GLU ARG TYR ILE ASP SER ASN GLY ARG GLU SEQRES 3 A 903 ARG THR ARG GLU VAL GLU TYR LYS PRO SER LEU PHE ALA SEQRES 4 A 903 HIS CYS PRO GLU SER GLN ALA THR LYS TYR PHE ASP ILE SEQRES 5 A 903 TYR GLY LYS PRO CYS THR ARG LYS LEU PHE ALA ASN MET SEQRES 6 A 903 ARG ASP ALA SER GLN TRP ILE LYS ARG MET GLU ASP ILE SEQRES 7 A 903 GLY LEU GLU ALA LEU GLY MET ASP ASP PHE LYS LEU ALA SEQRES 8 A 903 TYR LEU SER ASP THR TYR ASN TYR GLU ILE LYS TYR ASP SEQRES 9 A 903 HIS THR LYS ILE ARG VAL ALA ASN PHE ASP ILE GLU VAL SEQRES 10 A 903 THR SER PRO ASP GLY PHE PRO GLU PRO SER GLN ALA LYS SEQRES 11 A 903 HIS PRO ILE ASP ALA ILE THR HIS TYR ASP SER ILE ASP SEQRES 12 A 903 ASP ARG PHE TYR VAL PHE ASP LEU LEU ASN SER PRO TYR SEQRES 13 A 903 GLY ASN VAL GLU GLU TRP SER ILE GLU ILE ALA ALA LYS SEQRES 14 A 903 LEU GLN GLU GLN GLY GLY ASP GLU VAL PRO SER GLU ILE SEQRES 15 A 903 ILE ASP LYS ILE ILE TYR MET PRO PHE ASP ASN GLU LYS SEQRES 16 A 903 GLU LEU LEU MET GLU TYR LEU ASN PHE TRP GLN GLN LYS SEQRES 17 A 903 THR PRO VAL ILE LEU THR GLY TRP ASN VAL GLU SER PHE SEQRES 18 A 903 ALA ILE PRO TYR VAL TYR ASN ARG ILE LYS ASN ILE PHE SEQRES 19 A 903 GLY GLU SER THR ALA LYS ARG LEU SER PRO HIS ARG LYS SEQRES 20 A 903 THR ARG VAL LYS VAL ILE GLU ASN MET TYR GLY SER ARG SEQRES 21 A 903 GLU ILE ILE THR LEU PHE GLY ILE SER VAL LEU ASP TYR SEQRES 22 A 903 ILE ASP LEU TYR LYS LYS PHE SER PHE THR ASN GLN PRO SEQRES 23 A 903 SER TYR SER LEU ASP TYR ILE SER GLU PHE GLU LEU ASN SEQRES 24 A 903 VAL GLY LYS LEU LYS TYR ASP GLY PRO ILE SER LYS LEU SEQRES 25 A 903 ARG GLU SER ASN HIS GLN ARG TYR ILE SER TYR ASN ILE SEQRES 26 A 903 ILE ALA VAL TYR ARG VAL LEU GLN ILE ASP ALA LYS ARG SEQRES 27 A 903 GLN PHE ILE ASN LEU SER LEU ASP MET GLY TYR TYR ALA SEQRES 28 A 903 LYS ILE GLN ILE GLN SER VAL PHE SER PRO ILE LYS THR SEQRES 29 A 903 TRP ASP ALA ILE ILE PHE ASN SER LEU LYS GLU GLN ASN SEQRES 30 A 903 LYS VAL ILE PRO GLN GLY ARG SER HIS PRO VAL GLN PRO SEQRES 31 A 903 TYR PRO GLY ALA PHE VAL LYS GLU PRO ILE PRO ASN ARG SEQRES 32 A 903 TYR LYS TYR VAL MET SER PHE ASP LEU THR SER LEU TYR SEQRES 33 A 903 PRO SER ILE ILE ARG GLN VAL ASN ILE SER PRO GLU THR SEQRES 34 A 903 ILE ALA GLY THR PHE LYS VAL ALA PRO LEU HIS ASP TYR SEQRES 35 A 903 ILE ASN ALA VAL ALA GLU ARG PRO SER ASP VAL TYR SER SEQRES 36 A 903 CYS SER PRO ASN GLY MET MET TYR TYR LYS ASP ARG ASP SEQRES 37 A 903 GLY VAL VAL PRO THR GLU ILE THR LYS VAL PHE ASN GLN SEQRES 38 A 903 ARG LYS GLU HIS LYS GLY TYR MET LEU ALA ALA GLN ARG SEQRES 39 A 903 ASN GLY GLU ILE ILE LYS GLU ALA LEU HIS ASN PRO ASN SEQRES 40 A 903 LEU SER VAL ASP GLU PRO LEU ASP VAL ASP TYR ARG PHE SEQRES 41 A 903 ASP PHE SER ASP GLU ILE LYS GLU LYS ILE LYS LYS LEU SEQRES 42 A 903 SER ALA LYS SER LEU ASN GLU MET LEU PHE ARG ALA GLN SEQRES 43 A 903 ARG THR GLU VAL ALA GLY MET THR ALA GLN ILE ASN ARG SEQRES 44 A 903 LYS LEU LEU ILE ASN SER LEU TYR GLY ALA LEU GLY ASN SEQRES 45 A 903 VAL TRP PHE ARG TYR TYR ASP LEU ARG ASN ALA THR ALA SEQRES 46 A 903 ILE THR THR PHE GLY GLN MET ALA LEU GLN TRP ILE GLU SEQRES 47 A 903 ARG LYS VAL ASN GLU TYR LEU ASN GLU VAL CYS GLY THR SEQRES 48 A 903 GLU GLY GLU ALA PHE VAL LEU TYR GLY ASP THR ASP SER SEQRES 49 A 903 ILE TYR VAL SER ALA ASP LYS ILE ILE ASP LYS VAL GLY SEQRES 50 A 903 GLU SER LYS PHE ARG ASP THR ASN HIS TRP VAL ASP PHE SEQRES 51 A 903 LEU ASP LYS PHE ALA ARG GLU ARG MET GLU PRO ALA ILE SEQRES 52 A 903 ASP ARG GLY PHE ARG GLU MET CYS GLU TYR MET ASN ASN SEQRES 53 A 903 LYS GLN HIS LEU MET PHE MET ASP ARG GLU ALA ILE ALA SEQRES 54 A 903 GLY PRO PRO LEU GLY SER LYS GLY ILE GLY GLY PHE TRP SEQRES 55 A 903 THR GLY LYS LYS ARG TYR ALA LEU ASN VAL TRP ASP MET SEQRES 56 A 903 GLU GLY THR ARG TYR ALA GLU PRO LYS LEU LYS ILE MET SEQRES 57 A 903 GLY LEU GLU THR GLN LYS SER SER THR PRO LYS ALA VAL SEQRES 58 A 903 GLN LYS ALA LEU LYS GLU CYS ILE ARG ARG MET LEU GLN SEQRES 59 A 903 GLU GLY GLU GLU SER LEU GLN GLU TYR PHE LYS GLU PHE SEQRES 60 A 903 GLU LYS GLU PHE ARG GLN LEU ASN TYR ILE SER ILE ALA SEQRES 61 A 903 SER VAL SER SER ALA ASN ASN ILE ALA LYS TYR ASP VAL SEQRES 62 A 903 GLY GLY PHE PRO GLY PRO LYS CYS PRO PHE HIS ILE ARG SEQRES 63 A 903 GLY ILE LEU THR TYR ASN ARG ALA ILE LYS GLY ASN ILE SEQRES 64 A 903 ASP ALA PRO GLN VAL VAL GLU GLY GLU LYS VAL TYR VAL SEQRES 65 A 903 LEU PRO LEU ARG GLU GLY ASN PRO PHE GLY ASP LYS CYS SEQRES 66 A 903 ILE ALA TRP PRO SER GLY THR GLU ILE THR ASP LEU ILE SEQRES 67 A 903 LYS ASP ASP VAL LEU HIS TRP MET ASP TYR THR VAL LEU SEQRES 68 A 903 LEU GLU LYS THR PHE ILE LYS PRO LEU GLU GLY PHE THR SEQRES 69 A 903 SER ALA ALA LYS LEU ASP TYR GLU LYS LYS ALA SER LEU SEQRES 70 A 903 PHE ASP MET PHE ASP PHE MODRES 2OZM DDG P 14 DG HET 3DR T 3 11 HET DDG P 14 21 HET MG A 904 1 HET N5P A 905 32 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 N5P PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO- HETNAM 3 N5P PENTOFURANOSYL}-5-NITRO -1H-INDOLE HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN N5P 5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE FORMUL 1 3DR C5 H11 O6 P FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 4 MG MG 2+ FORMUL 5 N5P C13 H17 N2 O14 P3 FORMUL 6 HOH *400(H2 O) HELIX 1 1 ASN A 64 ASP A 77 1 14 HELIX 2 2 ASP A 87 TYR A 97 1 11 HELIX 3 3 ASP A 104 ILE A 108 5 5 HELIX 4 4 SER A 163 LYS A 169 1 7 HELIX 5 5 LEU A 170 GLY A 174 5 5 HELIX 6 6 PRO A 179 ASP A 184 1 6 HELIX 7 7 ASN A 193 LYS A 208 1 16 HELIX 8 8 PHE A 221 GLY A 235 1 15 HELIX 9 9 GLY A 235 LYS A 240 1 6 HELIX 10 10 ARG A 241 SER A 243 5 3 HELIX 11 11 ASP A 272 SER A 281 1 10 HELIX 12 12 SER A 289 ASN A 299 1 11 HELIX 13 13 LYS A 311 ASN A 316 1 6 HELIX 14 14 ASN A 316 GLN A 339 1 24 HELIX 15 15 GLN A 339 ALA A 351 1 13 HELIX 16 16 GLN A 354 PHE A 359 5 6 HELIX 17 17 SER A 360 GLU A 375 1 16 HELIX 18 18 SER A 414 ASN A 424 1 11 HELIX 19 19 PRO A 438 ASN A 444 1 7 HELIX 20 20 GLY A 469 GLU A 501 1 33 HELIX 21 21 SER A 523 LYS A 531 1 9 HELIX 22 22 SER A 534 GLY A 571 1 38 HELIX 23 23 ASP A 579 GLY A 610 1 32 HELIX 24 24 ALA A 629 LYS A 635 1 7 HELIX 25 25 ASP A 643 ARG A 658 1 16 HELIX 26 26 ARG A 658 ASN A 675 1 18 HELIX 27 27 LEU A 730 LYS A 734 5 5 HELIX 28 28 PRO A 738 GLU A 755 1 18 HELIX 29 29 GLY A 756 PHE A 771 1 16 HELIX 30 30 ARG A 772 LEU A 774 5 3 HELIX 31 31 ASN A 775 ALA A 780 5 6 HELIX 32 32 ILE A 788 PHE A 796 5 9 HELIX 33 33 PRO A 802 LYS A 816 1 15 HELIX 34 34 ILE A 858 MET A 866 1 9 HELIX 35 35 ASP A 867 PHE A 876 1 10 HELIX 36 36 PHE A 876 LYS A 888 1 13 HELIX 37 37 PHE A 898 ASP A 902 5 5 SHEET 1 A 3 PHE A 4 ILE A 11 0 SHEET 2 A 3 SER A 14 ILE A 20 -1 O ARG A 18 N LEU A 6 SHEET 3 A 3 GLU A 26 VAL A 31 -1 O ARG A 27 N TYR A 19 SHEET 1 B 2 SER A 36 HIS A 40 0 SHEET 2 B 2 CYS A 57 LEU A 61 -1 O THR A 58 N ALA A 39 SHEET 1 C 2 PHE A 50 ASP A 51 0 SHEET 2 C 2 LYS A 378 VAL A 379 1 O VAL A 379 N PHE A 50 SHEET 1 D 6 ILE A 186 MET A 189 0 SHEET 2 D 6 ARG A 145 ASP A 150 1 N PHE A 146 O ILE A 187 SHEET 3 D 6 ILE A 133 ASP A 140 -1 N HIS A 138 O TYR A 147 SHEET 4 D 6 VAL A 110 VAL A 117 -1 N ASN A 112 O TYR A 139 SHEET 5 D 6 ILE A 212 THR A 214 1 O ILE A 212 N ALA A 111 SHEET 6 D 6 SER A 269 VAL A 270 1 O SER A 269 N LEU A 213 SHEET 1 E 2 ASN A 153 SER A 154 0 SHEET 2 E 2 GLY A 157 ASN A 158 -1 O GLY A 157 N SER A 154 SHEET 1 F 2 THR A 248 VAL A 252 0 SHEET 2 F 2 GLU A 261 LEU A 265 -1 O THR A 264 N ARG A 249 SHEET 1 G 7 ASN A 402 ARG A 403 0 SHEET 2 G 7 GLY A 700 GLY A 704 -1 O TRP A 702 N ASN A 402 SHEET 3 G 7 ARG A 707 MET A 715 -1 O ARG A 707 N THR A 703 SHEET 4 G 7 MET A 683 ALA A 689 -1 N ILE A 688 O TRP A 713 SHEET 5 G 7 VAL A 407 LEU A 412 -1 N SER A 409 O GLU A 686 SHEET 6 G 7 SER A 624 SER A 628 -1 O VAL A 627 N MET A 408 SHEET 7 G 7 VAL A 617 TYR A 619 -1 N TYR A 619 O TYR A 626 SHEET 1 H 4 ASN A 402 ARG A 403 0 SHEET 2 H 4 GLY A 700 GLY A 704 -1 O TRP A 702 N ASN A 402 SHEET 3 H 4 ARG A 707 MET A 715 -1 O ARG A 707 N THR A 703 SHEET 4 H 4 THR A 718 MET A 728 -1 O LYS A 724 N VAL A 712 SHEET 1 I 3 ILE A 430 THR A 433 0 SHEET 2 I 3 MET A 461 TYR A 463 -1 O MET A 462 N ALA A 431 SHEET 3 I 3 SER A 455 SER A 457 -1 N SER A 455 O TYR A 463 SHEET 1 J 3 SER A 781 SER A 784 0 SHEET 2 J 3 LYS A 829 PRO A 834 -1 O VAL A 830 N SER A 783 SHEET 3 J 3 CYS A 845 PRO A 849 -1 O TRP A 848 N TYR A 831 LINK O3' DG T 2 P 3DR T 3 1555 1555 1.60 LINK O3' 3DR T 3 P DC T 4 1555 1555 1.60 LINK O3' DA P 13 P DDG P 14 1555 1555 1.59 LINK OD1 ASP A 411 MG MG A 904 1555 1555 2.13 LINK O LEU A 412 MG MG A 904 1555 1555 2.11 LINK OD2 ASP A 623 MG MG A 904 1555 1555 2.36 LINK MG MG A 904 O2A N5P A 905 1555 1555 2.43 LINK MG MG A 904 O2G N5P A 905 1555 1555 1.83 LINK MG MG A 904 O2B N5P A 905 1555 1555 2.02 SITE 1 AC1 4 ASP A 411 LEU A 412 ASP A 623 N5P A 905 SITE 1 AC2 17 ASP A 411 LEU A 412 THR A 413 SER A 414 SITE 2 AC2 17 LEU A 415 TYR A 416 ARG A 482 LYS A 560 SITE 3 AC2 17 ASN A 564 THR A 622 ASP A 623 MG A 904 SITE 4 AC2 17 HOH A1109 HOH A1181 DDG P 14 3DR T 3 SITE 5 AC2 17 DC T 4 CRYST1 81.232 117.492 126.142 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 0.012310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007928 0.00000