HEADER TRANSFERASE/DNA 04-OCT-06 2J6T
TITLE TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-
TITLE 2 METHYLGUANINE MODIFIED DNA, AND DATP.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE IV;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: POL IV;
COMPND 5 EC: 2.7.7.7;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3';
COMPND 9 CHAIN: P;
COMPND 10 SYNONYM: 13-MER PRIMER;
COMPND 11 ENGINEERED: YES;
COMPND 12 OTHER_DETAILS: 5'GGGGGAAGGATTC3';
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: 5'-D(*TP*CP*AP*TP*XP*GP*AP*AP*TP*CP
COMPND 15 *CP*TP*TP*CP*CP*CP*CP*C)-3';
COMPND 16 CHAIN: T;
COMPND 17 SYNONYM: 18-MER TEMPLATE;
COMPND 18 ENGINEERED: YES;
COMPND 19 OTHER_DETAILS: 5'TCAT G32 GAATCCTTCCCCC3'
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS;
SOURCE 3 ORGANISM_TAXID: 273057;
SOURCE 4 STRAIN: P2;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B/DPO4-NHIS;
SOURCE 10 OTHER_DETAILS: GENE DPO4;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES
KEYWDS TRANSFERASE-DNA COMPLEX, MUTATOR PROTEIN, DNA REPLICATION, O6-
KEYWDS 2 METHYLGUANINE, TRANSFERASE, METAL-BINDING, TRANSLESION DNA
KEYWDS 3 SYNTHESIS, DNA-DIRECTED DNA POLYMERASE, DPO4, DNA REPAIR, DNA
KEYWDS 4 DAMAGE, DNA-BINDING, NUCLEOTIDYLTRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.IRIMIA,R.L.EOFF,F.P.GUENGERICH,M.EGLI
REVDAT 7 13-DEC-23 2J6T 1 REMARK LINK
REVDAT 6 02-FEB-10 2J6T 1 VERSN
REVDAT 5 24-FEB-09 2J6T 1 VERSN
REVDAT 4 26-JUN-07 2J6T 1 REMARK
REVDAT 3 05-JUN-07 2J6T 1 REMARK
REVDAT 2 16-JAN-07 2J6T 1 JRNL
REVDAT 1 22-NOV-06 2J6T 0
JRNL AUTH R.L.EOFF,A.IRIMIA,M.EGLI,F.P.GUENGERICH
JRNL TITL SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 IS PARTIALLY
JRNL TITL 2 INHIBITED BY "WOBBLE" PAIRING BETWEEN O6- METHYLGUANINE AND
JRNL TITL 3 CYTOSINE, BUT ACCURATE BYPASS IS PREFERRED.
JRNL REF J.BIOL.CHEM. V. 282 1456 2007
JRNL REFN ISSN 0021-9258
JRNL PMID 17105728
JRNL DOI 10.1074/JBC.M609661200
REMARK 2
REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 986175.730
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 16550
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 SET) : 0.237
REMARK 3 FREE R VALUE : 0.269
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 812
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2554
REMARK 3 BIN R VALUE (WORKING SET) : 0.3750
REMARK 3 BIN FREE R VALUE : 0.3820
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2744
REMARK 3 NUCLEIC ACID ATOMS : 610
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 89
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 45.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.36000
REMARK 3 B22 (A**2) : -4.41000
REMARK 3 B33 (A**2) : 2.06000
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39
REMARK 3 ESD FROM SIGMAA (A) : 0.47
REMARK 3 LOW RESOLUTION CUTOFF (A) : 50.0
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.008
REMARK 3 BOND ANGLES (DEGREES) : 1.300
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.030
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.230 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.130 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.810 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.930 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.31
REMARK 3 BSOL : 30.10
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP1.PARAM
REMARK 3 PARAMETER FILE 3 : ATP.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : DNA-RNA1.TOP
REMARK 3 TOPOLOGY FILE 3 : ATP.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3 TOPOLOGY FILE 5 : WATER_REP.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2J6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-06.
REMARK 100 THE DEPOSITION ID IS D_1290030141.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-AUG-05
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.40
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : BRUKER MONTEL CONFOCAL
REMARK 200 MULTILAYER MIRRORS
REMARK 200 OPTICS : BRUKER MONTEL CONFOCAL
REMARK 200 MULTILAYER MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : BRUKER
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT
REMARK 200 DATA SCALING SOFTWARE : SAINT
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16550
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600
REMARK 200 RESOLUTION RANGE LOW (A) : 22.500
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 4.350
REMARK 200 R MERGE (I) : 0.11000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.26
REMARK 200 R MERGE FOR SHELL (I) : 0.97000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400
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 2BQR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.61
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 100 MM CA(CH3CO2)2, 50MM
REMARK 280 NACL, 5MM CACL2, AND 1MM DATP., PH 7.40
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
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 47.50600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.47450
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.50600
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.47450
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: 5800 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20040 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.2 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T
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 HIS A -5
REMARK 465 HIS A -4
REMARK 465 HIS A -3
REMARK 465 HIS A -2
REMARK 465 HIS A -1
REMARK 465 HIS A 0
REMARK 465 ALA A 343
REMARK 465 ILE A 344
REMARK 465 GLY A 345
REMARK 465 LEU A 346
REMARK 465 ASP A 347
REMARK 465 LYS A 348
REMARK 465 PHE A 349
REMARK 465 PHE A 350
REMARK 465 ASP A 351
REMARK 465 THR A 352
REMARK 465 DT T 1
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 GLU A 342 CA C O CB CG CD OE1
REMARK 470 GLU A 342 OE2
REMARK 470 DC T 2 P OP1 OP2
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 NH2 ARG A 336 O HOH A 2056 1.93
REMARK 500 NE ARG A 336 O HOH A 2058 2.04
REMARK 500 O HOH P 2003 O HOH P 2005 2.14
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 ARG A 247 NE - CZ - NH1 ANGL. DEV. = -3.0 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 10 51.31 18.46
REMARK 500 PHE A 11 -77.47 -28.85
REMARK 500 LYS A 24 127.14 -34.70
REMARK 500 ARG A 36 -105.02 -68.96
REMARK 500 PHE A 37 -157.60 -86.82
REMARK 500 ARG A 77 71.40 -117.27
REMARK 500 ASP A 105 23.80 -155.52
REMARK 500 ILE A 111 38.31 -95.12
REMARK 500 ASP A 113 41.84 -82.52
REMARK 500 LYS A 114 -16.56 -152.28
REMARK 500 PHE A 210 -76.05 -40.84
REMARK 500 ASP A 211 -38.50 -31.13
REMARK 500 ASN A 234 53.92 -149.06
REMARK 500 ASP A 277 75.68 32.53
REMARK 500 ASP A 292 38.76 -93.54
REMARK 500 LEU A 293 24.80 47.57
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 CA A1001 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD1
REMARK 620 2 PHE A 8 O 94.2
REMARK 620 3 ASP A 105 OD2 60.6 87.1
REMARK 620 4 DTP A1000 O1G 109.6 112.2 159.7
REMARK 620 5 DTP A1000 O1B 167.4 89.6 107.7 79.9
REMARK 620 6 DTP A1000 O5' 97.6 135.5 62.7 103.8 71.5
REMARK 620 7 HOH A2004 O 69.2 71.1 123.1 61.6 123.4 152.5
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1002 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD1
REMARK 620 2 ASP A 7 OD2 43.8
REMARK 620 3 ASP A 105 OD1 81.4 125.1
REMARK 620 4 GLU A 106 OE2 117.9 96.4 109.3
REMARK 620 5 DTP A1000 O5' 93.7 112.2 66.7 147.7
REMARK 620 6 HOH A2025 O 156.5 159.0 75.2 69.1 79.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1003 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 181 O
REMARK 620 2 ILE A 186 O 85.6
REMARK 620 3 HOH A2040 O 83.0 68.4
REMARK 620 4 HOH A2041 O 93.7 80.1 148.5
REMARK 620 5 HOH P2004 O 95.7 171.9 119.6 91.9
REMARK 620 6 HOH P2015 O 174.5 88.9 94.9 85.5 89.8
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 CA A 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1003
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A 1000
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1JX4 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX
REMARK 900 WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE
REMARK 900 RELATED ID: 1JXL RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX
REMARK 900 WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE
REMARK 900 RELATED ID: 1N48 RELATED DB: PDB
REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC
REMARK 900 LESION
REMARK 900 RELATED ID: 1N56 RELATED DB: PDB
REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC
REMARK 900 LESION
REMARK 900 RELATED ID: 1RYR RELATED DB: PDB
REMARK 900 REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION
REMARK 900 RELATED ID: 1RYS RELATED DB: PDB
REMARK 900 REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION
REMARK 900 RELATED ID: 1S0M RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCTIN A
REMARK 900 TERNARY COMPLEX WITH A DNA POLYMERASE
REMARK 900 RELATED ID: 1S0N RELATED DB: PDB
REMARK 900 SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS
REMARK 900 FOR BASE SUBSTITUTION AND FRAMESHIFT
REMARK 900 RELATED ID: 1S0O RELATED DB: PDB
REMARK 900 SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS
REMARK 900 FOR BASE SUBSTITUTION AND FRAMESHIFT
REMARK 900 RELATED ID: 1S10 RELATED DB: PDB
REMARK 900 SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS
REMARK 900 FOR BASE SUBSTITUTION AND FRAMESHIFT
REMARK 900 RELATED ID: 1S97 RELATED DB: PDB
REMARK 900 DPO4 WITH GT MISMATCH
REMARK 900 RELATED ID: 1S9F RELATED DB: PDB
REMARK 900 DPO WITH AT MATCHED
REMARK 900 RELATED ID: 2AGO RELATED DB: PDB
REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND
REMARK 900 PYROPHOSPHOROLYSIS
REMARK 900 RELATED ID: 2AGP RELATED DB: PDB
REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND
REMARK 900 PYROPHOSPHOROLYSIS
REMARK 900 RELATED ID: 2AGQ RELATED DB: PDB
REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND
REMARK 900 PYROPHOSPHOROLYSIS
REMARK 900 RELATED ID: 2ASD RELATED DB: PDB
REMARK 900 OXOG-MODIFIED INSERTION TERNARY COMPLEX
REMARK 900 RELATED ID: 2ASJ RELATED DB: PDB
REMARK 900 OXOG-MODIFIED PREINSERTION BINARY COMPLEX
REMARK 900 RELATED ID: 2ASL RELATED DB: PDB
REMARK 900 OXOG-MODIFIED POSTINSERTION BINARY COMPLEX
REMARK 900 RELATED ID: 2ATL RELATED DB: PDB
REMARK 900 UNMODIFIED INSERTION TERNARY COMPLEX
REMARK 900 RELATED ID: 2AU0 RELATED DB: PDB
REMARK 900 UNMODIFIED PREINSERTION BINARY COMPLEX
REMARK 900 RELATED ID: 2BQ3 RELATED DB: PDB
REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4.
REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION
REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
REMARK 900 RELATED ID: 2BQR RELATED DB: PDB
REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4.
REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION
REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
REMARK 900 RELATED ID: 2BQU RELATED DB: PDB
REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4.
REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION
REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
REMARK 900 RELATED ID: 2BR0 RELATED DB: PDB
REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4.
REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION
REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE
REMARK 900 RELATED ID: 2C22 RELATED DB: PDB
REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-
REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA
REMARK 900 POLYMERASE DPO4
REMARK 900 RELATED ID: 2C28 RELATED DB: PDB
REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-
REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA
REMARK 900 POLYMERASE DPO4
REMARK 900 RELATED ID: 2C2D RELATED DB: PDB
REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-
REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA
REMARK 900 POLYMERASE DPO4
REMARK 900 RELATED ID: 2C2E RELATED DB: PDB
REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-
REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA
REMARK 900 POLYMERASE DPO4
REMARK 900 RELATED ID: 2C2R RELATED DB: PDB
REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-
REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA RELATED
REMARK 900 ENTRIES
REMARK 900 RELATED ID: 2J6S RELATED DB: PDB
REMARK 900 TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-
REMARK 900 METHYLGUANINE MODIFIED DNA, AND DATP.
REMARK 900 RELATED ID: 2J6U RELATED DB: PDB
REMARK 900 TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-
REMARK 900 METHYLGUANINE MODIFIED DNA, AND DGTP.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 N-TERMINAL 6 HISTIDINE-TAG ADDED COMPARED TO UNIPROT
REMARK 999 Q97W02 SEQUENCE.
DBREF 2J6T A -5 0 PDB 2J6T 2J6T -5 0
DBREF 2J6T A 1 352 UNP Q97W02 DPO42_SULSO 1 352
DBREF 2J6T P 1 13 PDB 2J6T 2J6T 1 13
DBREF 2J6T T 1 18 PDB 2J6T 2J6T 1 18
SEQRES 1 A 358 HIS HIS HIS HIS HIS HIS MET ILE VAL LEU PHE VAL ASP
SEQRES 2 A 358 PHE ASP TYR PHE TYR ALA GLN VAL GLU GLU VAL LEU ASN
SEQRES 3 A 358 PRO SER LEU LYS GLY LYS PRO VAL VAL VAL CYS VAL PHE
SEQRES 4 A 358 SER GLY ARG PHE GLU ASP SER GLY ALA VAL ALA THR ALA
SEQRES 5 A 358 ASN TYR GLU ALA ARG LYS PHE GLY VAL LYS ALA GLY ILE
SEQRES 6 A 358 PRO ILE VAL GLU ALA LYS LYS ILE LEU PRO ASN ALA VAL
SEQRES 7 A 358 TYR LEU PRO MET ARG LYS GLU VAL TYR GLN GLN VAL SER
SEQRES 8 A 358 SER ARG ILE MET ASN LEU LEU ARG GLU TYR SER GLU LYS
SEQRES 9 A 358 ILE GLU ILE ALA SER ILE ASP GLU ALA TYR LEU ASP ILE
SEQRES 10 A 358 SER ASP LYS VAL ARG ASP TYR ARG GLU ALA TYR ASN LEU
SEQRES 11 A 358 GLY LEU GLU ILE LYS ASN LYS ILE LEU GLU LYS GLU LYS
SEQRES 12 A 358 ILE THR VAL THR VAL GLY ILE SER LYS ASN LYS VAL PHE
SEQRES 13 A 358 ALA LYS ILE ALA ALA ASP MET ALA LYS PRO ASN GLY ILE
SEQRES 14 A 358 LYS VAL ILE ASP ASP GLU GLU VAL LYS ARG LEU ILE ARG
SEQRES 15 A 358 GLU LEU ASP ILE ALA ASP VAL PRO GLY ILE GLY ASN ILE
SEQRES 16 A 358 THR ALA GLU LYS LEU LYS LYS LEU GLY ILE ASN LYS LEU
SEQRES 17 A 358 VAL ASP THR LEU SER ILE GLU PHE ASP LYS LEU LYS GLY
SEQRES 18 A 358 MET ILE GLY GLU ALA LYS ALA LYS TYR LEU ILE SER LEU
SEQRES 19 A 358 ALA ARG ASP GLU TYR ASN GLU PRO ILE ARG THR ARG VAL
SEQRES 20 A 358 ARG LYS SER ILE GLY ARG ILE VAL THR MET LYS ARG ASN
SEQRES 21 A 358 SER ARG ASN LEU GLU GLU ILE LYS PRO TYR LEU PHE ARG
SEQRES 22 A 358 ALA ILE GLU GLU SER TYR TYR LYS LEU ASP LYS ARG ILE
SEQRES 23 A 358 PRO LYS ALA ILE HIS VAL VAL ALA VAL THR GLU ASP LEU
SEQRES 24 A 358 ASP ILE VAL SER ARG GLY ARG THR PHE PRO HIS GLY ILE
SEQRES 25 A 358 SER LYS GLU THR ALA TYR SER GLU SER VAL LYS LEU LEU
SEQRES 26 A 358 GLN LYS ILE LEU GLU GLU ASP GLU ARG LYS ILE ARG ARG
SEQRES 27 A 358 ILE GLY VAL ARG PHE SER LYS PHE ILE GLU ALA ILE GLY
SEQRES 28 A 358 LEU ASP LYS PHE PHE ASP THR
SEQRES 1 P 13 DG DG DG DG DG DA DA DG DG DA DT DT DC
SEQRES 1 T 18 DT DC DA DT 6OG DG DA DA DT DC DC DT DT
SEQRES 2 T 18 DC DC DC DC DC
MODRES 2J6T 6OG T 5 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
HET 6OG T 5 23
HET DTP A1000 30
HET CA A1001 1
HET CA A1002 1
HET CA A1003 1
HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
HETNAM CA CALCIUM ION
FORMUL 3 6OG C11 H16 N5 O7 P
FORMUL 4 DTP C10 H16 N5 O12 P3
FORMUL 5 CA 3(CA 2+)
FORMUL 8 HOH *89(H2 O)
HELIX 1 1 TYR A 10 ASN A 20 1 11
HELIX 2 2 PRO A 21 LYS A 24 5 4
HELIX 3 3 ASN A 47 LYS A 52 1 6
HELIX 4 4 PRO A 60 LEU A 68 1 9
HELIX 5 5 ARG A 77 GLU A 94 1 18
HELIX 6 6 SER A 112 VAL A 115 5 4
HELIX 7 7 ASP A 117 GLU A 136 1 20
HELIX 8 8 ASN A 147 LYS A 159 1 13
HELIX 9 9 ASP A 167 LEU A 178 1 12
HELIX 10 10 ILE A 180 VAL A 183 5 4
HELIX 11 11 GLY A 187 LEU A 197 1 11
HELIX 12 12 LEU A 202 ILE A 208 5 7
HELIX 13 13 GLU A 209 GLY A 218 1 10
HELIX 14 14 GLY A 218 ARG A 230 1 13
HELIX 15 15 ASN A 257 ASP A 277 1 21
HELIX 16 16 SER A 307 ASP A 326 1 20
SHEET 1 AA 5 ILE A 99 SER A 103 0
SHEET 2 AA 5 GLU A 106 ASP A 110 -1 O GLU A 106 N SER A 103
SHEET 3 AA 5 VAL A 3 PHE A 8 -1 O LEU A 4 N LEU A 109
SHEET 4 AA 5 VAL A 140 SER A 145 -1 O THR A 141 N ASP A 7
SHEET 5 AA 5 ILE A 163 ILE A 166 1 O LYS A 164 N ILE A 144
SHEET 1 AB 3 GLY A 41 ALA A 46 0
SHEET 2 AB 3 VAL A 28 PHE A 33 -1 O VAL A 30 N ALA A 44
SHEET 3 AB 3 VAL A 72 PRO A 75 1 O VAL A 72 N VAL A 29
SHEET 1 AC 4 SER A 244 SER A 255 0
SHEET 2 AC 4 ILE A 330 PHE A 340 -1 O ILE A 330 N SER A 255
SHEET 3 AC 4 PRO A 281 THR A 290 -1 N LYS A 282 O LYS A 339
SHEET 4 AC 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288
LINK O3' DT T 4 P 6OG T 5 1555 1555 1.60
LINK O3' 6OG T 5 P DG T 6 1555 1555 1.60
LINK OD1 ASP A 7 CA CA A1001 1555 1555 2.64
LINK OD1 ASP A 7 CA CA A1002 1555 1555 2.85
LINK OD2 ASP A 7 CA CA A1002 1555 1555 3.04
LINK O PHE A 8 CA CA A1001 1555 1555 2.26
LINK OD2 ASP A 105 CA CA A1001 1555 1555 2.44
LINK OD1 ASP A 105 CA CA A1002 1555 1555 2.98
LINK OE2 GLU A 106 CA CA A1002 1555 1555 2.53
LINK O ALA A 181 CA CA A1003 1555 1555 2.42
LINK O ILE A 186 CA CA A1003 1555 1555 2.81
LINK O1G DTP A1000 CA CA A1001 1555 1555 2.93
LINK O1B DTP A1000 CA CA A1001 1555 1555 2.55
LINK O5' DTP A1000 CA CA A1001 1555 1555 3.03
LINK O5' DTP A1000 CA CA A1002 1555 1555 3.00
LINK CA CA A1001 O HOH A2004 1555 1555 2.61
LINK CA CA A1002 O HOH A2025 1555 1555 2.75
LINK CA CA A1003 O HOH A2040 1555 1555 2.70
LINK CA CA A1003 O HOH A2041 1555 1555 2.64
LINK CA CA A1003 O HOH P2004 1555 1555 2.55
LINK CA CA A1003 O HOH P2015 1555 1555 2.51
CISPEP 1 LYS A 159 PRO A 160 0 0.12
SITE 1 AC1 5 ASP A 7 PHE A 8 ASP A 105 DTP A1000
SITE 2 AC1 5 HOH A2004
SITE 1 AC2 5 ASP A 7 ASP A 105 GLU A 106 DTP A1000
SITE 2 AC2 5 HOH A2025
SITE 1 AC3 6 ALA A 181 ILE A 186 HOH A2040 HOH A2041
SITE 2 AC3 6 HOH P2004 HOH P2015
SITE 1 AC4 22 PHE A 8 ASP A 9 TYR A 10 PHE A 11
SITE 2 AC4 22 TYR A 12 ALA A 44 THR A 45 TYR A 48
SITE 3 AC4 22 ARG A 51 ALA A 57 ASP A 105 LYS A 159
SITE 4 AC4 22 CA A1001 CA A1002 HOH A2004 HOH A2013
SITE 5 AC4 22 HOH A2061 HOH A2062 HOH A2063 HOH A2064
SITE 6 AC4 22 DT T 4 6OG T 5
CRYST1 95.012 102.949 53.013 90.00 90.00 90.00 P 21 21 2 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 0.010525 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009714 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018863 0.00000
(ATOM LINES ARE NOT SHOWN.)
END