10 20 30 40 50 60 70 80 1N56 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 04-NOV-02 1N56
TITLE Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAINING TITLE 2 ABASIC LESION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)- COMPND 3 3'; COMPND 4 CHAIN: C, E; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: TEMPLATE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*TP*CP*AP*TP*(3DR) COMPND 9 P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'; COMPND 10 CHAIN: D, F; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA POLYMERASE IV; COMPND 15 CHAIN: A, B; COMPND 16 SYNONYM: DPO4, POL IV, REPAIR DNA POLYMERASE OF THE COMPND 17 DINB/UMUC SUPERFAMILY, DINP; COMPND 18 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 7 ORGANISM_TAXID: 2287; SOURCE 8 GENE: DPO4; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET22BB
KEYWDS Y-FAMILY, DNA POLYMERASE, DNA LESION BYPASS, PROTEIN-DNA KEYWDS 2 COMPLEX, TRANSFERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR H.LING,F.BOUDSOCQ,R.WOODGATE,W.YANG
REVDAT 2 24-FEB-09 1N56 1 VERSN REVDAT 1 24-FEB-04 1N56 0
JRNL AUTH H.LING,F.BOUDSOCQ,R.WOODGATE,W.YANG JRNL TITL A Y-FAMILY POLYMERASE COMPLEXED WITH ABASIC JRNL TITL 2 LESIONS: CATCHING DNA WITH A LOADED NUCLEOSIDE JRNL TITL 3 TRIPHOSPHATE JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.LING,F.BOUDSOCQ,R.WOODGATE,W.YANG REMARK 1 TITL CRYSTAL STRUCTURE OF A Y-FAMILYDNA POLYMERASE IN REMARK 1 TITL 2 ACTION: A MECHANISM FOR ERROR-PRONE AND REMARK 1 TITL 3 LESION-BYPASS REPLICATION REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 107 91 2001 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 11595180 REMARK 1 DOI 10.1016/S0092-8674(01)00515-3
REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 2.3 REMARK 3 NUMBER OF REFLECTIONS : 39503 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) : 0.225 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 980 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5486 REMARK 3 NUCLEIC ACID ATOMS : 1238 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 497 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.27 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1N56 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017531.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.0 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 : RIGAKU RU200HB REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39503 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : 0.03800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39900 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: CNS REMARK 200 STARTING MODEL: 1JX4 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3350, 0.1M HEPES, 100MM REMARK 280 CALCIUM ACETATE, 2.5% GLYCEROL, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 49.00800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.83000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.83000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.00800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.17900 REMARK 290 SMTRY3 4 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 APPLY THE FOLLOWING TO CHAINS: C, D, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 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 GLU A 342 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 GLU B 342 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 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 O3' DA E 1814 O HOH E 783 2.03 REMARK 500 OP1 DA E 1814 O HOH E 649 2.05 REMARK 500 O3' ATP A 1803 O HOH A 936 2.08 REMARK 500 OD1 ASP B 105 O HOH E 649 2.11 REMARK 500 O LEU A 4 O HOH A 919 2.19 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 DA C1814 O3' DA C1814 C3' -0.046 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 DA C1814 N9 - C1' - C2' ANGL. DEV. = -13.3 DEGREES REMARK 500 DA C1814 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT F1902 C3' - C2' - C1' ANGL. DEV. = -5.1 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 53.92 21.65 REMARK 500 ASN A 20 72.52 -152.75 REMARK 500 SER A 96 128.82 -176.49 REMARK 500 ASP A 113 34.31 -94.03 REMARK 500 SER A 145 -161.78 -170.70 REMARK 500 LYS A 196 18.50 -69.42 REMARK 500 LEU A 197 12.58 -145.53 REMARK 500 ASN A 234 52.08 -165.39 REMARK 500 SER A 255 174.49 174.57 REMARK 500 ASP A 277 86.28 38.02 REMARK 500 LYS A 278 -28.65 85.63 REMARK 500 LEU A 293 -5.62 90.06 REMARK 500 TYR B 10 49.57 23.94 REMARK 500 ASN B 20 70.54 -156.17 REMARK 500 SER B 96 125.42 -179.22 REMARK 500 ASP B 105 20.56 -143.93 REMARK 500 SER B 145 -163.84 -166.28 REMARK 500 LYS B 196 17.49 -68.30 REMARK 500 LEU B 197 11.40 -143.23 REMARK 500 ASP B 204 -9.40 -58.16 REMARK 500 ARG B 256 26.91 -151.27 REMARK 500 ASP B 277 83.12 35.51 REMARK 500 LYS B 278 -10.94 78.23 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 C1814 0.09 SIDE_CHAIN REMARK 500 DA E1814 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ATP A 1803 REMARK 610 ATP B 1804
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 106 OE2 REMARK 620 2 ASP A 7 OD1 102.8 REMARK 620 3 ATP A1803 O1A 150.8 77.6 REMARK 620 4 HOH A 648 O 67.1 127.2 89.2 REMARK 620 5 HOH A1023 O 92.5 65.5 113.2 157.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A1803 O1G REMARK 620 2 ASP A 7 OD1 113.7 REMARK 620 3 ASP A 7 OD2 73.8 52.8 REMARK 620 4 PHE A 8 O 122.6 108.1 105.1 REMARK 620 5 ASP A 105 OD2 147.1 69.4 121.7 83.7 REMARK 620 6 HOH A 666 O 109.1 127.2 175.5 70.4 57.9 REMARK 620 7 ATP A1803 O1A 72.2 84.3 103.7 150.4 75.7 80.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 799 O REMARK 620 2 HOH B 915 O 61.4 REMARK 620 3 HOH E 649 O 179.1 119.4 REMARK 620 4 ATP B1804 O1A 107.1 75.5 73.7 REMARK 620 5 GLU B 106 OE1 68.6 69.1 111.1 141.5 REMARK 620 6 DA E1814 OP2 100.4 54.1 79.9 97.2 49.3 REMARK 620 7 ASP B 105 OD2 111.5 147.2 68.1 76.8 141.4 147.9 REMARK 620 8 ASP B 7 OD1 62.0 116.6 117.6 96.3 112.6 160.4 49.9 REMARK 620 9 ASP B 105 OD1 137.4 159.8 41.8 100.1 107.8 108.1 44.3 83.2 REMARK 620 10 DA E1814 OP1 138.5 105.3 41.2 106.6 70.0 51.7 99.2 REMARK 620 136.1 56.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 9 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B1804 O3A REMARK 620 2 HOH B 812 O 67.3 REMARK 620 3 ATP B1804 O1A 46.3 95.8 REMARK 620 4 HOH B 822 O 143.0 120.3 143.7 REMARK 620 5 ATP B1804 O1G 68.5 123.8 76.9 80.0 REMARK 620 6 ASP B 105 OD2 95.3 56.2 81.9 119.5 158.7 REMARK 620 7 PHE B 8 O 119.0 63.3 159.2 57.1 114.0 85.6 REMARK 620 8 ASP B 7 OD2 133.5 158.6 98.2 48.6 75.4 110.1 101.7 REMARK 620 9 ASP B 7 OD1 132.0 115.7 87.3 80.1 119.4 60.9 101.1 49.3 REMARK 620 N 1 2 3 4 5 6 7 8
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 401 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 403 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 404 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1803 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 1804
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JX4 RELATED DB: PDB REMARK 900 THIS PROTEIN IN COMPLEXED WITH UNDAMAGED DNA. REMARK 900 RELATED ID: 1JXL RELATED DB: PDB REMARK 900 THIS PROTEIN IN COMPLEXED WITH UNDAMAGED DNA. REMARK 900 RELATED ID: 1N48 RELATED DB: PDB REMARK 900 1N48 CONTAINS THE PROTEIN/DNA STRUCTURE WHICH IS IN THE REMARK 900 REACTION STAGE JUST BEFORE BYPASSING THE ABASIC LESION
DBREF 1N56 A 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 1N56 B 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 1N56 C 1801 1814 PDB 1N56 1N56 1801 1814 DBREF 1N56 D 1902 1918 PDB 1N56 1N56 1902 1918 DBREF 1N56 E 1801 1814 PDB 1N56 1N56 1801 1814 DBREF 1N56 F 1902 1918 PDB 1N56 1N56 1902 1918
SEQRES 1 C 14 DG DG DG DG DG DA DA DG DG DA DC DT DA SEQRES 2 C 14 DA SEQRES 1 D 17 DT DC DA DT 3DR DA DG DT DC DC DT DT DC SEQRES 2 D 17 DC DC DC DC SEQRES 1 E 14 DG DG DG DG DG DA DA DG DG DA DC DT DA SEQRES 2 E 14 DA SEQRES 1 F 17 DT DC DA DT 3DR DA DG DT DC DC DT DT DC SEQRES 2 F 17 DC DC DC DC SEQRES 1 A 352 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 A 352 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 A 352 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 A 352 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 352 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 A 352 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 A 352 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 A 352 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 A 352 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 A 352 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 A 352 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 A 352 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 A 352 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 A 352 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 A 352 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 A 352 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 A 352 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 A 352 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 A 352 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 A 352 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 A 352 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 A 352 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 A 352 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 A 352 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 A 352 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 A 352 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 A 352 LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS PHE PHE ASP SEQRES 28 A 352 THR SEQRES 1 B 352 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 B 352 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 B 352 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 B 352 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 B 352 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 B 352 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 B 352 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 B 352 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 B 352 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 B 352 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 B 352 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 B 352 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 B 352 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 B 352 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 B 352 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 B 352 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 B 352 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 B 352 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 B 352 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 B 352 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 B 352 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 B 352 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 B 352 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 B 352 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 B 352 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 B 352 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 B 352 LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS PHE PHE ASP SEQRES 28 B 352 THR
HET 3DR D1906 11 HET 3DR F1906 11 HET MG A 401 1 HET CA B 403 1 HET MG A 402 1 HET MG B 404 1 HET ATP A1803 30 HET ATP B1804 30
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
HETSYN 3DR ABASIC DIDEOXYRIBOSE
FORMUL 2 3DR 2(C5 H11 O6 P) FORMUL 7 MG 3(MG 2+) FORMUL 8 CA CA 2+ FORMUL 11 ATP 2(C10 H16 N5 O13 P3) FORMUL 13 HOH *497(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 ASP A 117 LYS A 137 1 21 HELIX 7 7 ASN A 147 LYS A 159 1 13 HELIX 8 8 ASP A 167 LEU A 178 1 12 HELIX 9 9 ASP A 179 VAL A 183 5 5 HELIX 10 10 GLY A 187 LYS A 196 1 10 HELIX 11 11 VAL A 203 ILE A 208 1 6 HELIX 12 12 GLU A 209 GLY A 218 1 10 HELIX 13 13 GLY A 218 ARG A 230 1 13 HELIX 14 14 ASN A 257 ASP A 277 1 21 HELIX 15 15 SER A 307 ASP A 326 1 20 HELIX 16 16 TYR B 10 LEU B 19 1 10 HELIX 17 17 ASN B 20 LYS B 24 5 5 HELIX 18 18 ASN B 47 LYS B 52 1 6 HELIX 19 19 PRO B 60 LEU B 68 1 9 HELIX 20 20 ARG B 77 GLU B 94 1 18 HELIX 21 21 ASP B 117 LYS B 137 1 21 HELIX 22 22 ASN B 147 LYS B 159 1 13 HELIX 23 23 ASP B 167 LEU B 178 1 12 HELIX 24 24 ASP B 179 VAL B 183 5 5 HELIX 25 25 GLY B 187 LYS B 196 1 10 HELIX 26 26 VAL B 203 ILE B 208 1 6 HELIX 27 27 GLU B 209 GLY B 218 1 10 HELIX 28 28 GLY B 218 ARG B 230 1 13 HELIX 29 29 ASN B 257 ASP B 277 1 21 HELIX 30 30 SER B 307 ASP B 326 1 20
SHEET 1 A 5 ILE A 99 SER A 103 0 SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100 SHEET 3 A 5 VAL A 3 PHE A 8 -1 N LEU A 4 O LEU A 109 SHEET 4 A 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5 SHEET 5 A 5 ILE A 163 VAL A 165 1 O LYS A 164 N ILE A 144 SHEET 1 B 3 GLY A 41 ALA A 46 0 SHEET 2 B 3 VAL A 28 PHE A 33 -1 N VAL A 30 O ALA A 44 SHEET 3 B 3 VAL A 72 PRO A 75 1 O LEU A 74 N CYS A 31 SHEET 1 C 4 SER A 244 SER A 255 0 SHEET 2 C 4 ILE A 330 PHE A 340 -1 O ILE A 330 N SER A 255 SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 332 SHEET 4 C 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 SHEET 1 D 5 ILE B 99 SER B 103 0 SHEET 2 D 5 GLU B 106 ASP B 110 -1 O TYR B 108 N GLU B 100 SHEET 3 D 5 VAL B 3 PHE B 8 -1 N LEU B 4 O LEU B 109 SHEET 4 D 5 VAL B 140 SER B 145 -1 O SER B 145 N VAL B 3 SHEET 5 D 5 ILE B 163 VAL B 165 1 O LYS B 164 N ILE B 144 SHEET 1 E 3 GLY B 41 ALA B 46 0 SHEET 2 E 3 VAL B 28 PHE B 33 -1 N VAL B 30 O ALA B 44 SHEET 3 E 3 VAL B 72 PRO B 75 1 O VAL B 72 N VAL B 29 SHEET 1 F 4 SER B 244 SER B 255 0 SHEET 2 F 4 ILE B 330 PHE B 340 -1 O PHE B 337 N ILE B 245 SHEET 3 F 4 PRO B 281 THR B 290 -1 N VAL B 289 O ARG B 331 SHEET 4 F 4 ILE B 295 THR B 301 -1 O VAL B 296 N ALA B 288
LINK MG MG A 401 OE2 GLU A 106 1555 1555 1.78 LINK MG MG A 401 OD1 ASP A 7 1555 1555 2.72 LINK MG MG A 401 O1A ATP A1803 1555 1555 2.23 LINK MG MG A 401 O HOH A 648 1555 1555 2.26 LINK MG MG A 401 O HOH A1023 1555 1555 2.42 LINK MG MG A 402 O1G ATP A1803 1555 1555 2.17 LINK MG MG A 402 OD1 ASP A 7 1555 1555 2.33 LINK MG MG A 402 OD2 ASP A 7 1555 1555 2.54 LINK MG MG A 402 O PHE A 8 1555 1555 2.24 LINK MG MG A 402 OD2 ASP A 105 1555 1555 2.48 LINK MG MG A 402 O HOH A 666 1555 1555 2.62 LINK MG MG A 402 O1A ATP A1803 1555 1555 2.33 LINK CA CA B 403 O HOH B 799 1555 1555 3.39 LINK CA CA B 403 O HOH B 915 1555 1555 2.40 LINK CA CA B 403 O HOH E 649 1555 1555 3.11 LINK CA CA B 403 O1A ATP B1804 1555 1555 2.23 LINK CA CA B 403 OE1 GLU B 106 1555 1555 2.28 LINK CA CA B 403 OP2 DA E1814 1555 1555 3.24 LINK CA CA B 403 OD2 ASP B 105 1555 1555 3.04 LINK CA CA B 403 OD1 ASP B 7 1555 1555 2.54 LINK CA CA B 403 OD1 ASP B 105 1555 1555 2.70 LINK CA CA B 403 OP1 DA E1814 1555 1555 2.36 LINK MG MG B 404 O3A ATP B1804 1555 1555 3.06 LINK MG MG B 404 O HOH B 812 1555 1555 2.52 LINK MG MG B 404 O1A ATP B1804 1555 1555 2.74 LINK MG MG B 404 O HOH B 822 1555 1555 2.84 LINK MG MG B 404 O1G ATP B1804 1555 1555 2.49 LINK MG MG B 404 OD2 ASP B 105 1555 1555 2.33 LINK MG MG B 404 O PHE B 8 1555 1555 2.21 LINK MG MG B 404 OD2 ASP B 7 1555 1555 2.76 LINK MG MG B 404 OD1 ASP B 7 1555 1555 2.40 LINK O3' DT D1905 P 3DR D1906 1555 1555 1.61 LINK O3' 3DR D1906 P DA D1907 1555 1555 1.61 LINK O3' DT F1905 P 3DR F1906 1555 1555 1.60 LINK O3' 3DR F1906 P DA F1907 1555 1555 1.59
CISPEP 1 LYS A 159 PRO A 160 0 0.02 CISPEP 2 LYS B 159 PRO B 160 0 -0.20
SITE 1 AC1 6 ASP A 7 GLU A 106 MG A 402 HOH A 648 SITE 2 AC1 6 HOH A1023 ATP A1803 SITE 1 AC2 7 ASP B 7 ASP B 105 GLU B 106 MG B 404 SITE 2 AC2 7 HOH B 915 ATP B1804 DA E1814 SITE 1 AC3 6 ASP A 7 PHE A 8 ASP A 105 MG A 401 SITE 2 AC3 6 HOH A 666 ATP A1803 SITE 1 AC4 7 ASP B 7 PHE B 8 ASP B 105 CA B 403 SITE 2 AC4 7 HOH B 812 HOH B 822 ATP B1804 SITE 1 AC5 21 ASP A 7 ASP A 9 TYR A 10 PHE A 11 SITE 2 AC5 21 TYR A 12 ALA A 44 THR A 45 TYR A 48 SITE 3 AC5 21 ARG A 51 ALA A 57 GLY A 58 ASP A 105 SITE 4 AC5 21 LYS A 159 MG A 401 MG A 402 HOH A 666 SITE 5 AC5 21 HOH A 808 HOH A 936 HOH C 804 DA C1814 SITE 6 AC5 21 DT D1905 SITE 1 AC6 21 ASP B 7 PHE B 8 ASP B 9 TYR B 10 SITE 2 AC6 21 PHE B 11 TYR B 12 ALA B 44 THR B 45 SITE 3 AC6 21 TYR B 48 ARG B 51 ASP B 105 LYS B 159 SITE 4 AC6 21 CA B 403 MG B 404 HOH B 677 HOH B 812 SITE 5 AC6 21 HOH B 915 HOH B 934 HOH E 649 DA E1814 SITE 6 AC6 21 DT F1905
CRYST1 98.016 102.358 105.660 90.00 90.00 90.00 P 21 21 21 8
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 0.010202 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009770 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009464 0.00000