HEADER POLYMERASE 29-SEP-05 2C2R
TITLE EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-
TITLE 2 DIHYDRO-8-OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE
TITLE 3 DPO4
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 ENGINEERED: YES;
COMPND 11 OTHER_DETAILS: 13-MER PRIMER EXTENDED BY POLYMERASE TO A 14-MER;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: 5'-D(*TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP
COMPND 14 *TP*TP*CP*CP*CP*CP*C)-3';
COMPND 15 CHAIN: T;
COMPND 16 ENGINEERED: YES;
COMPND 17 OTHER_DETAILS: 18-MER TEMPLATE
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 POLYMERASE, P2 DNA POLYMERASE IV, 7, 8-DIHYDRO-8-OXODEOXYGUANOSINE,
KEYWDS 2 TRANSLESION DNA POLYMERASE, NUCLEOTIDYLTRANSFERASE, TRANSFERASE, DNA
KEYWDS 3 DAMAGE, DNA REPAIR, DNA REPLICATION, DNA- BINDING, DNA-DIRECTED DNA
KEYWDS 4 POLYMERASE, MAGNESIUM, CALCIUM, METAL-BINDING, MUTATOR PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR A.IRIMIA,L.V.LOUKACHEVITCH,M.EGLI
REVDAT 4 13-DEC-23 2C2R 1 LINK
REVDAT 3 24-FEB-09 2C2R 1 VERSN
REVDAT 2 25-JAN-06 2C2R 1 JRNL
REVDAT 1 29-NOV-05 2C2R 0
JRNL AUTH H.ZANG,A.IRIMIA,J.-Y.CHOI,K.C.ANGEL,L.V.LOUKACHEVITCH,
JRNL AUTH 2 M.EGLI,F.P.GUENGERICH
JRNL TITL EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE
JRNL TITL 2 7,8-DIHYDRO-8-OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS
JRNL TITL 3 DNA POLYMERASE DPO4
JRNL REF J.BIOL.CHEM. V. 281 2358 2006
JRNL REFN ISSN 0021-9258
JRNL PMID 16306039
JRNL DOI 10.1074/JBC.M510889200
REMARK 2
REMARK 2 RESOLUTION. 2.55 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) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.99
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1203084.410
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 16645
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) : 0.251
REMARK 3 FREE R VALUE : 0.310
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 817
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011
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) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.90
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2463
REMARK 3 BIN R VALUE (WORKING SET) : 0.3760
REMARK 3 BIN FREE R VALUE : 0.3850
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.034
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2744
REMARK 3 NUCLEIC ACID ATOMS : 608
REMARK 3 HETEROGEN ATOMS : 31
REMARK 3 SOLVENT ATOMS : 106
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 55.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.60
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 27.67000
REMARK 3 B22 (A**2) : -18.88000
REMARK 3 B33 (A**2) : -8.79000
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) : 0.41
REMARK 3 ESD FROM SIGMAA (A) : 0.49
REMARK 3 LOW RESOLUTION CUTOFF (A) : 47.0
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.53
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.50
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.430
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) : 1.290 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.230 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.710 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.650 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.33
REMARK 3 BSOL : 64.67
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-RNA1.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : DCT.PARAM
REMARK 3 PARAMETER FILE 5 : ION.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 : WATER_REP.TOP
REMARK 3 TOPOLOGY FILE 4 : DCT.TOP
REMARK 3 TOPOLOGY FILE 5 : ION.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2C2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-05.
REMARK 100 THE DEPOSITION ID IS D_1290025826.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-AUG-05
REMARK 200 TEMPERATURE (KELVIN) : 110.0
REMARK 200 PH : 7.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 17-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16653
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 42.990
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 200 DATA REDUNDANCY : 3.640
REMARK 200 R MERGE (I) : 0.12000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2C28
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.05
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 3350,0.010 M TRIS-HCL PH 7.5,
REMARK 280 100 MM CA(CH3CO2)2, 1.25% GLYCEROL, 30 MM NACL, PH 7.50
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 47.60000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.07500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.60000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.07500
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: PQS
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 400
REMARK 400 COMPOUND
REMARK 400 INVOLVEMENT IN UNTARGETED MUTAGENESIS.
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 465 DC T 2
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 DA T 3 P OP1 OP2
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 DA T 3 C4'
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 OE1 GLU A 309 O HOH A 2058 1.95
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 8OG T 5 O3' - P - OP2 ANGL. DEV. = -14.4 DEGREES
REMARK 500 8OG T 5 O3' - P - OP1 ANGL. DEV. = -17.4 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 48.85 17.29
REMARK 500 PHE A 11 -70.27 -32.87
REMARK 500 PRO A 21 1.53 -59.17
REMARK 500 PHE A 37 144.98 169.93
REMARK 500 LEU A 68 73.39 -113.02
REMARK 500 ARG A 93 -5.98 -50.60
REMARK 500 SER A 96 99.49 160.09
REMARK 500 GLU A 97 29.92 -74.56
REMARK 500 ASP A 105 14.72 -143.26
REMARK 500 ASP A 113 -85.73 -61.05
REMARK 500 LYS A 114 -32.14 -23.47
REMARK 500 ASP A 117 144.47 109.70
REMARK 500 SER A 145 -168.43 -173.04
REMARK 500 ASN A 161 43.86 33.34
REMARK 500 ASP A 167 -171.63 -60.00
REMARK 500 LYS A 196 -75.41 -51.82
REMARK 500 LEU A 197 -11.25 -44.68
REMARK 500 ASN A 200 -11.59 -142.87
REMARK 500 THR A 205 -5.12 -58.74
REMARK 500 LYS A 214 -22.99 -39.47
REMARK 500 ASP A 231 16.32 50.96
REMARK 500 TYR A 233 -83.20 -80.46
REMARK 500 ASN A 234 106.01 39.65
REMARK 500 THR A 239 -62.03 -21.24
REMARK 500 ARG A 240 129.73 59.88
REMARK 500 SER A 255 175.04 175.03
REMARK 500 ARG A 256 16.82 -149.22
REMARK 500 LYS A 262 -60.99 -22.72
REMARK 500 ASP A 277 88.58 56.19
REMARK 500 LYS A 278 -43.05 72.89
REMARK 500 GLU A 327 -60.24 -128.91
REMARK 500 ARG A 328 150.25 -29.41
REMARK 500 ARG A 331 -61.16 -105.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 DA T 8 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2004 DISTANCE = 5.86 ANGSTROMS
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 A1343 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD2
REMARK 620 2 ASP A 105 OD1 122.9
REMARK 620 3 ASP A 105 OD2 97.3 47.1
REMARK 620 4 GLU A 106 OE2 80.5 109.2 149.7
REMARK 620 5 DCT A1342 O1A 105.0 127.6 111.7 97.8
REMARK 620 6 CA A1344 CA 66.6 93.4 46.3 146.7 86.6
REMARK 620 7 DOC P 14 OP2 144.2 90.6 116.4 76.2 53.0 129.3
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1344 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD1
REMARK 620 2 PHE A 8 O 62.7
REMARK 620 3 ASP A 105 OD2 116.2 100.9
REMARK 620 4 DCT A1342 O3A 121.7 144.1 106.3
REMARK 620 5 DCT A1342 O2G 74.1 96.9 162.1 56.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1345 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 181 O
REMARK 620 2 ILE A 186 O 104.5
REMARK 620 3 HOH P2019 O 123.4 75.2
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1346 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DCT A1342 O1A
REMARK 620 2 HOH A2067 O 44.8
REMARK 620 3 DOC P 14 OP1 57.1 90.1
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1343
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1344
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1345
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1346
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCT A1342
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: 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 999
REMARK 999 SEQUENCE
REMARK 999 THE 14TH NUCLEOTIDE WAS ADDED BY POLYMERASE
DBREF 2C2R A -5 0 PDB 2C2R 2C2R -5 0
DBREF 2C2R A 1 352 UNP Q97W02 DPO42_SULSO 1 352
DBREF 2C2R P 1 14 PDB 2C2R 2C2R 1 14
DBREF 2C2R T 1 18 PDB 2C2R 2C2R 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 14 DG DG DG DG DG DA DA DG DG DA DT DT DC
SEQRES 2 P 14 DOC
SEQRES 1 T 18 DT DC DA DC 8OG DG DA DA DT DC DC DT DT
SEQRES 2 T 18 DC DC DC DC DC
MODRES 2C2R DOC P 14 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
MODRES 2C2R 8OG T 5 DG
HET DOC P 14 18
HET 8OG T 5 23
HET DCT A1342 27
HET CA A1343 1
HET CA A1344 1
HET CA A1345 1
HET CA A1346 1
HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
HETNAM CA CALCIUM ION
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
FORMUL 2 DOC C9 H14 N3 O6 P
FORMUL 3 8OG C10 H14 N5 O8 P
FORMUL 4 DCT C9 H16 N3 O12 P3
FORMUL 5 CA 4(CA 2+)
FORMUL 9 HOH *106(H2 O)
HELIX 1 1 TYR A 10 ASN A 20 1 11
HELIX 2 2 ASN A 47 LYS A 52 1 6
HELIX 3 3 PRO A 60 LEU A 68 1 9
HELIX 4 4 ARG A 77 ARG A 93 1 17
HELIX 5 5 TYR A 122 LYS A 137 1 16
HELIX 6 6 ASN A 147 LYS A 159 1 13
HELIX 7 7 GLU A 169 LEU A 178 1 10
HELIX 8 8 ILE A 180 VAL A 183 5 4
HELIX 9 9 GLY A 187 GLY A 198 1 12
HELIX 10 10 LEU A 202 SER A 207 5 6
HELIX 11 11 GLU A 209 ILE A 217 1 9
HELIX 12 12 GLY A 218 ARG A 230 1 13
HELIX 13 13 ASN A 257 ASP A 277 1 21
HELIX 14 14 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 VAL A 165 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 SER A 338
SHEET 4 AC 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288
LINK O3' DC P 13 P DOC P 14 1555 1555 1.61
LINK O3' DC T 4 P 8OG T 5 1555 1555 1.62
LINK O3' 8OG T 5 P DG T 6 1555 1555 1.59
LINK OD2 ASP A 7 CA CA A1343 1555 1555 2.67
LINK OD1 ASP A 7 CA CA A1344 1555 1555 2.84
LINK O PHE A 8 CA CA A1344 1555 1555 2.40
LINK OD1 ASP A 105 CA CA A1343 1555 1555 2.79
LINK OD2 ASP A 105 CA CA A1343 1555 1555 2.64
LINK OD2 ASP A 105 CA CA A1344 1555 1555 2.30
LINK OE2 GLU A 106 CA CA A1343 1555 1555 2.37
LINK O ALA A 181 CA CA A1345 1555 1555 2.55
LINK O ILE A 186 CA CA A1345 1555 1555 2.49
LINK O1A DCT A1342 CA CA A1343 1555 1555 3.01
LINK O3A DCT A1342 CA CA A1344 1555 1555 3.14
LINK O2G DCT A1342 CA CA A1344 1555 1555 2.15
LINK O1A DCT A1342 CA CA A1346 1555 1555 3.11
LINK CA CA A1343 CA CA A1344 1555 1555 3.11
LINK CA CA A1343 OP2 DOC P 14 1555 1555 2.59
LINK CA CA A1345 O HOH P2019 1555 1555 3.12
LINK CA CA A1346 O HOH A2067 1555 1555 2.81
LINK CA CA A1346 OP1 DOC P 14 1555 1555 2.50
CISPEP 1 LYS A 159 PRO A 160 0 0.04
SITE 1 AC1 6 ASP A 7 ASP A 105 GLU A 106 DCT A1342
SITE 2 AC1 6 CA A1344 DOC P 14
SITE 1 AC2 5 ASP A 7 PHE A 8 ASP A 105 DCT A1342
SITE 2 AC2 5 CA A1343
SITE 1 AC3 2 ALA A 181 ILE A 186
SITE 1 AC4 3 DCT A1342 HOH A2067 DOC P 14
SITE 1 AC5 21 ASP A 7 PHE A 8 ASP A 9 TYR A 10
SITE 2 AC5 21 TYR A 12 ALA A 44 TYR A 48 ARG A 51
SITE 3 AC5 21 ALA A 57 GLY A 58 LYS A 159 CA A1343
SITE 4 AC5 21 CA A1344 CA A1346 HOH A2065 HOH A2066
SITE 5 AC5 21 HOH A2067 DC P 13 DOC P 14 8OG T 5
SITE 6 AC5 21 DG T 6
CRYST1 95.200 100.150 52.000 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 0.010504 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009985 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019231 0.00000
(ATOM LINES ARE NOT SHOWN.)
END