HEADER TRANSFERASE/DNA 22-JAN-09 2W9C TITLE TERNARY COMPLEX OF DPO4 BOUND TO N2,N2-DIMETHYL-DEOXYGUANOSINE TITLE 2 MODIFIED DNA WITH INCOMING DTTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL IV, DPO4; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA POLYMERASE IV; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: POL IV, DPO4; COMPND 12 EC: 2.7.7.7; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'; COMPND 17 CHAIN: C, D; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: 13 BASE PRIMER DNA 5'-GGG GGA AGG ATT (DOC)- 3'; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP COMPND 22 *TP*TP*CP*CP*CP*CP*C)-3'; COMPND 23 CHAIN: E, F; COMPND 24 SYNONYM: TEMPLATE DNA; COMPND 25 ENGINEERED: YES; COMPND 26 OTHER_DETAILS: 18 BASE TEMPLATE DNA 5'-TCA C(M2G)G AAT CCT TCC CCC-3' SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: P2; SOURCE 5 ATCC: 35092; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 12 ORGANISM_TAXID: 273057; SOURCE 13 STRAIN: P2; SOURCE 14 ATCC: 35092; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES KEYWDS DNA-DIRECTED DNA POLYMERASE, N2-DIMETHYL-G, METAL-BINDING, MUTATOR KEYWDS 2 PROTEIN, DNA DAMAGE, DNA REPAIR, DNA-BINDING, TRANSFERASE, DNA KEYWDS 3 REPLICATION, NUCLEOTIDYLTRANSFERASE, TRANSFERASE/DNA, DNA, DPO4, KEYWDS 4 ADDUCT, CYTOPLASM, MAGNESIUM, POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.L.EOFF,H.ZHANG,I.D.KOSEKOV,C.J.RIZZO,M.EGLI,F.P.GUENGERICH REVDAT 3 13-DEC-23 2W9C 1 REMARK LINK REVDAT 2 30-JUN-09 2W9C 1 JRNL REMARK REVDAT 1 12-MAY-09 2W9C 0 JRNL AUTH H.ZHANG,R.L.EOFF,I.D.KOSEKOV,C.J.RIZZO,M.EGLI,F.P.GUENGERICH JRNL TITL STRUCTURE-FUNCTION RELATIONSHIPS IN MISCODING BY SULFOLOBUS JRNL TITL 2 SOLFATARICUS DNA POLYMERASE DPO4: GUANINE N2,N2-DIMETHYL JRNL TITL 3 SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE JRNL TITL 4 COMPLEXES. JRNL REF J.BIOL.CHEM. V. 284 17687 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19542237 JRNL DOI 10.1074/JBC.M109014274 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 44076.060 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.252 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1055 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) : 2.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5490 REMARK 3 NUCLEIC ACID ATOMS : 1180 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.01000 REMARK 3 B22 (A**2) : -19.45000 REMARK 3 B33 (A**2) : 29.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 30.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.270 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) : 1.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.580 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 64.62 REMARK 3 REMARK 3 NCS MODEL : NONE 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : DTTP.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-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : DTTP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : WATER.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2W9C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1290038624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20782 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 28.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2ASD REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO, REMARK 280 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE REMARK 280 GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM REMARK 280 CHLORIDE, 1 MM DTTP. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 50.81100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E 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 350 REMARK 350 BIOMOLECULE: 2 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: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 ALA B 343 REMARK 465 ILE B 344 REMARK 465 GLY B 345 REMARK 465 LEU B 346 REMARK 465 ASP B 347 REMARK 465 LYS B 348 REMARK 465 PHE B 349 REMARK 465 PHE B 350 REMARK 465 ASP B 351 REMARK 465 THR B 352 REMARK 465 DT E 1 REMARK 465 DC E 2 REMARK 465 DT F 1 REMARK 465 DC F 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 GLU B 342 CA C O CB CG CD OE1 REMARK 470 GLU B 342 OE2 REMARK 470 DA E 3 P OP1 OP2 REMARK 470 DA F 3 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 O1B TTP B 1345 O HOH B 2038 1.91 REMARK 500 O4' DC F 18 O HOH F 2006 1.98 REMARK 500 O HOH A 2021 O HOH A 2022 2.01 REMARK 500 OP2 DT F 12 O HOH F 2005 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 176 O5' DA F 3 2656 1.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC F 4 O3' DC F 4 C3' -0.039 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 B 256 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 256 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 O2G E 5 C3' - O3' - P ANGL. DEV. = -8.1 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 10 48.11 23.34 REMARK 500 PHE A 11 -74.69 -34.47 REMARK 500 ASN A 20 74.90 158.82 REMARK 500 PRO A 21 -14.71 -49.29 REMARK 500 LYS A 24 93.86 -50.79 REMARK 500 ARG A 36 -82.87 -48.11 REMARK 500 THR A 45 147.65 177.59 REMARK 500 ASN A 47 -177.06 -69.82 REMARK 500 LYS A 52 12.29 -57.66 REMARK 500 GLU A 94 44.52 -74.79 REMARK 500 TYR A 95 -1.25 -154.47 REMARK 500 SER A 96 129.91 160.66 REMARK 500 SER A 103 -152.16 -117.82 REMARK 500 LEU A 109 -162.21 -118.01 REMARK 500 ASP A 110 57.21 -174.20 REMARK 500 ILE A 111 34.39 -63.66 REMARK 500 ASP A 113 -77.08 -86.07 REMARK 500 LYS A 114 -38.01 -34.84 REMARK 500 ASP A 117 169.88 93.39 REMARK 500 TYR A 122 -17.50 -48.95 REMARK 500 SER A 145 -177.24 -173.90 REMARK 500 ASN A 147 -169.35 -119.74 REMARK 500 LYS A 164 147.24 -170.88 REMARK 500 ASP A 167 151.97 -39.70 REMARK 500 VAL A 171 9.47 -65.68 REMARK 500 GLU A 192 -62.27 -95.63 REMARK 500 ASN A 200 -69.53 -142.22 REMARK 500 LEU A 202 -86.84 -40.92 REMARK 500 VAL A 203 -32.91 -22.83 REMARK 500 LEU A 213 -75.45 -78.74 REMARK 500 LYS A 214 -56.47 -19.86 REMARK 500 ASP A 231 -8.31 67.02 REMARK 500 GLU A 232 -76.94 -62.07 REMARK 500 TYR A 233 -91.41 34.67 REMARK 500 ASN A 234 96.71 39.60 REMARK 500 THR A 239 -36.62 -30.98 REMARK 500 ARG A 240 144.27 54.40 REMARK 500 SER A 244 147.76 169.82 REMARK 500 LEU A 258 -1.25 -43.58 REMARK 500 LYS A 262 -60.62 -26.31 REMARK 500 GLU A 271 25.96 -70.55 REMARK 500 SER A 272 -37.74 -137.56 REMARK 500 ASP A 277 112.15 0.91 REMARK 500 LEU A 293 52.79 31.87 REMARK 500 ARG A 300 122.11 165.50 REMARK 500 PHE B 8 81.42 -51.70 REMARK 500 ASP B 9 123.21 -29.54 REMARK 500 TYR B 10 64.51 30.51 REMARK 500 ASN B 20 71.72 -174.95 REMARK 500 PRO B 27 104.47 -46.53 REMARK 500 REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS. 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 E 8 0.06 SIDE CHAIN REMARK 500 DG F 6 0.05 SIDE CHAIN REMARK 500 DT F 9 0.06 SIDE CHAIN REMARK 500 DC F 10 0.08 SIDE CHAIN 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 A1343 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 62.6 REMARK 620 3 ASP A 105 OD2 115.2 127.8 REMARK 620 4 TTP A1345 O1G 115.7 82.1 128.7 REMARK 620 5 TTP A1345 O3B 114.4 136.6 93.9 59.6 REMARK 620 6 TTP A1345 O1B 60.5 116.5 100.6 98.9 57.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1342 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 105 OD2 REMARK 620 2 TTP A1345 O1A 101.9 REMARK 620 3 HOH A2021 O 102.1 125.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1344 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 ILE A 186 O 110.2 REMARK 620 3 HOH A2029 O 79.5 102.7 REMARK 620 4 HOH A2030 O 83.4 148.0 108.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1343 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD2 REMARK 620 2 TTP B1345 O1G 139.6 REMARK 620 3 TTP B1345 O1B 90.9 51.4 REMARK 620 4 TTP B1345 O2G 138.2 67.7 93.7 REMARK 620 5 HOH B2001 O 85.7 128.6 131.8 60.9 REMARK 620 6 HOH B2036 O 134.9 82.8 133.8 58.4 69.3 REMARK 620 7 HOH B2037 O 61.9 112.6 75.7 79.1 60.4 125.5 REMARK 620 8 HOH B2038 O 79.7 65.9 51.6 133.2 165.2 120.1 113.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1342 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 103 OG REMARK 620 2 ASP B 105 OD2 80.7 REMARK 620 3 GLU B 106 OE1 102.7 93.2 REMARK 620 4 HOH B2015 O 91.4 107.5 156.7 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. 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 1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A 1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP B 1345 REMARK 900 REMARK 900 RELATED ENTRIES 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: 2ASL RELATED DB: PDB REMARK 900 OXOG-MODIFIED POSTINSERTION BINARY COMPLEX REMARK 900 RELATED ID: 2JEG RELATED DB: PDB REMARK 900 THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE REMARK 900 INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS REMARK 900 DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND REMARK 900 X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING REMARK 900 RELATED ID: 1RYS RELATED DB: PDB REMARK 900 REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION REMARK 900 RELATED ID: 2V4S RELATED DB: PDB REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2- NAPHTHYL-GUANINE ADDUCT REMARK 900 IN SYN ORIENTATION REMARK 900 RELATED ID: 2J6T 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: 2W9B RELATED DB: PDB REMARK 900 BINARY COMPLEX OF DPO4 BOUND TO N2,N2- DIMETHYL-DEOXYGUANOSINE REMARK 900 MODIFIED DNA 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: 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: 2ATL RELATED DB: PDB REMARK 900 UNMODIFIED INSERTION TERNARY COMPLEX 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: 2VA2 RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX REMARK 900 CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE REMARK 900 NUCLEOTIDE IN THE TEMPLATE STRAND REMARK 900 RELATED ID: 1S97 RELATED DB: PDB REMARK 900 DPO4 WITH GT MISMATCH 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: 2AGO RELATED DB: PDB REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND REMARK 900 PYROPHOSPHOROLYSIS REMARK 900 RELATED ID: 2JEJ RELATED DB: PDB REMARK 900 THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE REMARK 900 INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS REMARK 900 DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND REMARK 900 X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING REMARK 900 RELATED ID: 2ASJ RELATED DB: PDB REMARK 900 OXOG-MODIFIED PREINSERTION BINARY COMPLEX REMARK 900 RELATED ID: 2ASD RELATED DB: PDB REMARK 900 OXOG-MODIFIED INSERTION TERNARY COMPLEX REMARK 900 RELATED ID: 2W9A RELATED DB: PDB REMARK 900 TERNARY COMPLEX OF DPO4 BOUND TO N2,N2- DIMETHYL-DEOXYGUANOSINE REMARK 900 MODIFIED DNA WITH INCOMING DGTP 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: 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: 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: 2J6U RELATED DB: PDB REMARK 900 TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6- REMARK 900 METHYLGUANINE MODIFIED DNA, AND DGTP. REMARK 900 RELATED ID: 2UVU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG REMARK 900 CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 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: 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: 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 REMARK 900 POLYMERASE DPO4 REMARK 900 RELATED ID: 2JEF RELATED DB: PDB REMARK 900 THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOTIDE TRIPHOSPHATE REMARK 900 INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS REMARK 900 DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE AND X-RAY REMARK 900 CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING 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: 2W8L RELATED DB: PDB REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2- NAPHTHYL-GUANINE ADDUCT REMARK 900 IN ANTI ORIENTATION REMARK 900 RELATED ID: 2UVW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG REMARK 900 CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 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: 2JEI RELATED DB: PDB REMARK 900 THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE REMARK 900 INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS REMARK 900 DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND REMARK 900 X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING 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: 2AU0 RELATED DB: PDB REMARK 900 UNMODIFIED PREINSERTION BINARY COMPLEX REMARK 900 RELATED ID: 1S9F RELATED DB: PDB REMARK 900 DPO WITH AT MATCHED 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: 2V9W RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX REMARK 900 CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE REMARK 900 NUCLEOTIDE IN THE TEMPLATE STRAND REMARK 900 RELATED ID: 2V4R RELATED DB: PDB REMARK 900 NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH REMARK 900 DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE REMARK 900 CYTOSINE 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: 1RYR RELATED DB: PDB REMARK 900 REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION REMARK 900 RELATED ID: 2UVV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG REMARK 900 CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 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: 2V4Q RELATED DB: PDB REMARK 900 POST-INSERTION COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH REMARK 900 M1DG CONTAINING TEMPLATE DNA 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: 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: 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: 2UVR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG REMARK 900 CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS REMARK 900 RELATED ID: 2VA3 RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX REMARK 900 CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE REMARK 900 NUCLEOTIDE IN THE TEMPLATE STRAND REMARK 900 RELATED ID: 2W8K RELATED DB: PDB REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2- NAPHTHYL-GUANINE ADDUCT REMARK 900 IN SYN ORIENTATION REMARK 900 RELATED ID: 2V4T RELATED DB: PDB REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2- NAPHTHYL-GUANINE ADDUCT REMARK 900 IN ANTI ORIENTATION REMARK 999 REMARK 999 SEQUENCE REMARK 999 ENGINEERED HEXA-HISTIDINE TAG AND LAST 11 RESIDUES ARE REMARK 999 DISORDERED DBREF 2W9C A -5 0 PDB 2W9C 2W9C -5 0 DBREF 2W9C A 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 2W9C B -5 0 PDB 2W9C 2W9C -5 0 DBREF 2W9C B 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 2W9C C 1 13 PDB 2W9C 2W9C 1 13 DBREF 2W9C D 1 13 PDB 2W9C 2W9C 1 13 DBREF 2W9C E 1 18 PDB 2W9C 2W9C 1 18 DBREF 2W9C F 1 18 PDB 2W9C 2W9C 1 18 SEQADV 2W9C ARG A 223 UNP Q97W02 LYS 223 CONFLICT 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 ARG 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 B 358 HIS HIS HIS HIS HIS HIS MET ILE VAL LEU PHE VAL ASP SEQRES 2 B 358 PHE ASP TYR PHE TYR ALA GLN VAL GLU GLU VAL LEU ASN SEQRES 3 B 358 PRO SER LEU LYS GLY LYS PRO VAL VAL VAL CYS VAL PHE SEQRES 4 B 358 SER GLY ARG PHE GLU ASP SER GLY ALA VAL ALA THR ALA SEQRES 5 B 358 ASN TYR GLU ALA ARG LYS PHE GLY VAL LYS ALA GLY ILE SEQRES 6 B 358 PRO ILE VAL GLU ALA LYS LYS ILE LEU PRO ASN ALA VAL SEQRES 7 B 358 TYR LEU PRO MET ARG LYS GLU VAL TYR GLN GLN VAL SER SEQRES 8 B 358 SER ARG ILE MET ASN LEU LEU ARG GLU TYR SER GLU LYS SEQRES 9 B 358 ILE GLU ILE ALA SER ILE ASP GLU ALA TYR LEU ASP ILE SEQRES 10 B 358 SER ASP LYS VAL ARG ASP TYR ARG GLU ALA TYR ASN LEU SEQRES 11 B 358 GLY LEU GLU ILE LYS ASN LYS ILE LEU GLU LYS GLU LYS SEQRES 12 B 358 ILE THR VAL THR VAL GLY ILE SER LYS ASN LYS VAL PHE SEQRES 13 B 358 ALA LYS ILE ALA ALA ASP MET ALA LYS PRO ASN GLY ILE SEQRES 14 B 358 LYS VAL ILE ASP ASP GLU GLU VAL LYS ARG LEU ILE ARG SEQRES 15 B 358 GLU LEU ASP ILE ALA ASP VAL PRO GLY ILE GLY ASN ILE SEQRES 16 B 358 THR ALA GLU LYS LEU LYS LYS LEU GLY ILE ASN LYS LEU SEQRES 17 B 358 VAL ASP THR LEU SER ILE GLU PHE ASP LYS LEU LYS GLY SEQRES 18 B 358 MET ILE GLY GLU ALA LYS ALA LYS TYR LEU ILE SER LEU SEQRES 19 B 358 ALA ARG ASP GLU TYR ASN GLU PRO ILE ARG THR ARG VAL SEQRES 20 B 358 ARG LYS SER ILE GLY ARG ILE VAL THR MET LYS ARG ASN SEQRES 21 B 358 SER ARG ASN LEU GLU GLU ILE LYS PRO TYR LEU PHE ARG SEQRES 22 B 358 ALA ILE GLU GLU SER TYR TYR LYS LEU ASP LYS ARG ILE SEQRES 23 B 358 PRO LYS ALA ILE HIS VAL VAL ALA VAL THR GLU ASP LEU SEQRES 24 B 358 ASP ILE VAL SER ARG GLY ARG THR PHE PRO HIS GLY ILE SEQRES 25 B 358 SER LYS GLU THR ALA TYR SER GLU SER VAL LYS LEU LEU SEQRES 26 B 358 GLN LYS ILE LEU GLU GLU ASP GLU ARG LYS ILE ARG ARG SEQRES 27 B 358 ILE GLY VAL ARG PHE SER LYS PHE ILE GLU ALA ILE GLY SEQRES 28 B 358 LEU ASP LYS PHE PHE ASP THR SEQRES 1 C 13 DG DG DG DG DG DA DA DG DG DA DT DT DOC SEQRES 1 D 13 DG DG DG DG DG DA DA DG DG DA DT DT DOC SEQRES 1 E 18 DT DC DA DC O2G DG DA DA DT DC DC DT DT SEQRES 2 E 18 DC DC DC DC DC SEQRES 1 F 18 DT DC DA DC O2G DG DA DA DT DC DC DT DT SEQRES 2 F 18 DC DC DC DC DC MODRES 2W9C DOC C 13 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE MODRES 2W9C DOC D 13 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE MODRES 2W9C O2G E 5 G MODRES 2W9C O2G F 5 G HET DOC C 13 18 HET DOC D 13 18 HET O2G E 5 24 HET O2G F 5 24 HET MG A1342 1 HET MG A1343 1 HET MG A1344 1 HET TTP A1345 29 HET MG B1342 1 HET MG B1343 1 HET MG B1344 1 HET TTP B1345 29 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM O2G 2'-DEOXY-N,N-DIMETHYL-5'-O-[OXIDO(OXO) HETNAM 2 O2G PHOSPHONIO]GUANOSINE HETNAM MG MAGNESIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE FORMUL 3 DOC 2(C9 H14 N3 O6 P) FORMUL 5 O2G 2(C12 H18 N5 O7 P) FORMUL 7 MG 6(MG 2+) FORMUL 10 TTP 2(C10 H17 N2 O14 P3) FORMUL 15 HOH *109(H2 O) HELIX 1 1 TYR A 10 LEU A 19 1 10 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 GLU A 94 1 18 HELIX 5 5 GLU A 120 GLU A 136 1 17 HELIX 6 6 LYS A 148 LYS A 159 1 12 HELIX 7 7 GLY A 187 LEU A 197 1 11 HELIX 8 8 LEU A 202 SER A 207 5 6 HELIX 9 9 GLU A 209 ARG A 230 1 22 HELIX 10 10 ASN A 257 ASP A 277 1 21 HELIX 11 11 SER A 307 ASP A 326 1 20 HELIX 12 12 TYR B 10 LEU B 19 1 10 HELIX 13 13 ASN B 47 LYS B 52 1 6 HELIX 14 14 PRO B 60 LEU B 68 1 9 HELIX 15 15 ARG B 77 ASN B 90 1 14 HELIX 16 16 ASP B 117 LYS B 135 1 19 HELIX 17 17 ASN B 147 MET B 157 1 11 HELIX 18 18 GLU B 169 LEU B 178 1 10 HELIX 19 19 GLY B 187 LEU B 197 1 11 HELIX 20 20 VAL B 203 ILE B 208 5 6 HELIX 21 21 GLU B 209 ILE B 217 1 9 HELIX 22 22 GLY B 218 ARG B 230 1 13 HELIX 23 23 ILE B 261 ASP B 277 1 17 HELIX 24 24 SER B 307 SER B 315 1 9 HELIX 25 25 SER B 315 GLU B 324 1 10 SHEET 1 AA 4 GLU A 106 ALA A 107 0 SHEET 2 AA 4 VAL A 3 PHE A 8 -1 O VAL A 6 N ALA A 107 SHEET 3 AA 4 VAL A 140 SER A 145 -1 O THR A 141 N ASP A 7 SHEET 4 AA 4 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 LEU A 74 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 ASP A 294 THR A 301 -1 O ASP A 294 N THR A 290 SHEET 1 BA 5 ILE B 99 SER B 103 0 SHEET 2 BA 5 GLU B 106 ASP B 110 -1 O GLU B 106 N SER B 103 SHEET 3 BA 5 VAL B 3 ASP B 7 -1 O LEU B 4 N LEU B 109 SHEET 4 BA 5 THR B 141 SER B 145 -1 O THR B 141 N ASP B 7 SHEET 5 BA 5 ILE B 163 VAL B 165 1 O LYS B 164 N ILE B 144 SHEET 1 BB 3 GLY B 41 ALA B 46 0 SHEET 2 BB 3 VAL B 28 PHE B 33 -1 O VAL B 30 N ALA B 44 SHEET 3 BB 3 VAL B 72 PRO B 75 1 O VAL B 72 N VAL B 29 SHEET 1 BC 3 SER B 244 GLY B 246 0 SHEET 2 BC 3 ILE B 330 SER B 338 -1 O PHE B 337 N ILE B 245 SHEET 3 BC 3 VAL B 249 SER B 255 -1 O VAL B 249 N ILE B 333 SHEET 1 BD 4 SER B 244 GLY B 246 0 SHEET 2 BD 4 ILE B 330 SER B 338 -1 O PHE B 337 N ILE B 245 SHEET 3 BD 4 ALA B 283 THR B 290 -1 O ALA B 283 N SER B 338 SHEET 4 BD 4 ILE B 295 THR B 301 -1 O VAL B 296 N ALA B 288 LINK O3' DT C 12 P DOC C 13 1555 1555 1.58 LINK O3' DT D 12 P DOC D 13 1555 1555 1.59 LINK O3' DC E 4 P O2G E 5 1555 1555 1.57 LINK O3' O2G E 5 P DG E 6 1555 1555 1.60 LINK O3' DC F 4 P O2G F 5 1555 1555 1.58 LINK O3' O2G F 5 P DG F 6 1555 1555 1.61 LINK OD1 ASP A 7 MG MG A1343 1555 1555 2.77 LINK O PHE A 8 MG MG A1343 1555 1555 2.24 LINK OD2 ASP A 105 MG MG A1342 1555 1555 2.37 LINK OD2 ASP A 105 MG MG A1343 1555 1555 2.12 LINK O ALA A 181 MG MG A1344 1555 1555 2.38 LINK O ILE A 186 MG MG A1344 1555 1555 1.70 LINK MG MG A1342 O1A TTP A1345 1555 1555 2.55 LINK MG MG A1342 O HOH A2021 1555 1555 1.94 LINK MG MG A1343 O1G TTP A1345 1555 1555 1.99 LINK MG MG A1343 O3B TTP A1345 1555 1555 2.88 LINK MG MG A1343 O1B TTP A1345 1555 1555 2.40 LINK MG MG A1344 O HOH A2029 1555 1555 2.22 LINK MG MG A1344 O HOH A2030 1555 1555 2.41 LINK OD2 ASP B 7 MG MG B1343 1555 1555 2.50 LINK OG SER B 103 MG MG B1342 1555 1555 2.37 LINK OD2 ASP B 105 MG MG B1342 1555 1555 1.97 LINK OE1 GLU B 106 MG MG B1342 1555 1555 1.93 LINK MG MG B1342 O HOH B2015 1555 1555 2.45 LINK MG MG B1343 O1G TTP B1345 1555 1555 2.16 LINK MG MG B1343 O1B TTP B1345 1555 1555 2.11 LINK MG MG B1343 O2G TTP B1345 1555 1555 2.46 LINK MG MG B1343 O HOH B2001 1555 1555 2.21 LINK MG MG B1343 O HOH B2036 1555 1555 2.04 LINK MG MG B1343 O HOH B2037 1555 1555 2.24 LINK MG MG B1343 O HOH B2038 1555 1555 2.26 LINK MG MG B1344 O HOH B2025 1555 1555 2.10 CISPEP 1 LYS A 159 PRO A 160 0 -0.10 CISPEP 2 LYS B 159 PRO B 160 0 -0.04 SITE 1 AC1 4 ASP A 105 GLU A 106 TTP A1345 HOH A2021 SITE 1 AC2 4 ASP A 7 PHE A 8 ASP A 105 TTP A1345 SITE 1 AC3 5 ALA A 181 ILE A 186 HOH A2029 HOH A2030 SITE 2 AC3 5 DOC C 13 SITE 1 AC4 5 SER B 103 ASP B 105 GLU B 106 HOH B2015 SITE 2 AC4 5 HOH B2039 SITE 1 AC5 6 ASP B 7 TTP B1345 HOH B2001 HOH B2036 SITE 2 AC5 6 HOH B2037 HOH B2038 SITE 1 AC6 4 ALA B 181 ASP B 182 HOH B2024 HOH B2025 SITE 1 AC7 16 ASP A 7 PHE A 8 ASP A 9 TYR A 10 SITE 2 AC7 16 PHE A 11 THR A 45 ARG A 51 ALA A 57 SITE 3 AC7 16 ASP A 105 LYS A 159 MG A1342 MG A1343 SITE 4 AC7 16 HOH A2043 DOC C 13 O2G E 5 DG E 6 SITE 1 AC8 19 ASP B 7 PHE B 8 TYR B 10 PHE B 11 SITE 2 AC8 19 ALA B 44 ARG B 51 ALA B 57 ASP B 105 SITE 3 AC8 19 LYS B 159 MG B1343 HOH B2001 HOH B2036 SITE 4 AC8 19 HOH B2037 HOH B2038 HOH B2039 HOH B2040 SITE 5 AC8 19 DOC D 13 O2G F 5 DG F 6 CRYST1 51.707 101.622 96.753 90.00 92.29 90.00 P 1 21 1 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 0.019340 0.000000 0.000773 0.00000 SCALE2 0.000000 0.009840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010344 0.00000