PDB Short entry for 1SKR HEADER TRANSFERASE/ELECTRON TRANSPORT/DNA 05-MAR-04 1SKR TITLE T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE AND DDATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP* COMPND 3 CP*CP*AP*(2DA))-3'; COMPND 4 CHAIN: P; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DNA PRIMER; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*CP*CP*CP*TP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP COMPND 9 *CP*GP*TP*TP*TP*TP*CP*G)-3'; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA TEMPLATE; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA POLYMERASE; COMPND 15 CHAIN: A; COMPND 16 SYNONYM: T7 DNA POLYMERASE; COMPND 17 EC: 2.7.7.7; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: THIOREDOXIN 1; COMPND 22 CHAIN: B; COMPND 23 SYNONYM: TRX1, TRX; COMPND 24 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: ENTEROBACTERIA PHAGE T7; SOURCE 7 ORGANISM_TAXID: 10760; SOURCE 8 GENE: 5; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 4; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 562; SOURCE 14 GENE: TRXA, TSNC, FIPA, B3781, C4701, Z5291, ECS4714, STM3915, SOURCE 15 STMD1.75, STY3639, T3381, SF3854, S3905; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, UV-LESION, REPLICATION, OPEN, CLOSE, TRANSFERASE- KEYWDS 2 ELECTRON TRANSPORT-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,S.DUTTA,S.DOUBLIE,H.M.BDOUR,J.S.TAYLOR,T.ELLENBERGER REVDAT 5 14-FEB-24 1SKR 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 1SKR 1 REMARK REVDAT 3 24-FEB-09 1SKR 1 VERSN REVDAT 2 03-AUG-04 1SKR 1 JRNL AUTHOR REVDAT 1 06-JUL-04 1SKR 0 JRNL AUTH Y.LI,S.DUTTA,S.DOUBLIE,H.M.BDOUR,J.S.TAYLOR,T.ELLENBERGER JRNL TITL NUCLEOTIDE INSERTION OPPOSITE A CIS-SYN THYMINE DIMER BY A JRNL TITL 2 REPLICATIVE DNA POLYMERASE FROM BACTERIOPHAGE T7. JRNL REF NAT.STRUCT.MOL.BIOL. V. 11 784 2004 JRNL REFN ISSN 1545-9993 JRNL PMID 15235589 JRNL DOI 10.1038/NSMB792 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 44960 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2253 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 : 6110 REMARK 3 NUCLEIC ACID ATOMS : 489 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 381 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 1SKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021796. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44960 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, ACES, REMARK 280 ETHYLENE GLYCOL, DTT , PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 52.75300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 107.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.75300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 107.01000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, A, 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 DC P 1 REMARK 465 DG P 2 REMARK 465 DA P 3 REMARK 465 DA P 4 REMARK 465 DA P 5 REMARK 465 DA P 6 REMARK 465 DC P 7 REMARK 465 DG P 8 REMARK 465 DA P 9 REMARK 465 DC P 10 REMARK 465 DG P 11 REMARK 465 DC T 1 REMARK 465 DC T 2 REMARK 465 DC T 16 REMARK 465 DG T 17 REMARK 465 DT T 18 REMARK 465 DC T 19 REMARK 465 DG T 20 REMARK 465 DT T 21 REMARK 465 DT T 22 REMARK 465 DT T 23 REMARK 465 DT T 24 REMARK 465 DC T 25 REMARK 465 DG T 26 REMARK 465 PHE A 298 REMARK 465 LYS A 299 REMARK 465 LYS A 300 REMARK 465 PRO A 301 REMARK 465 LYS A 302 REMARK 465 ASN A 303 REMARK 465 LYS A 304 REMARK 465 ALA A 305 REMARK 465 GLN A 306 REMARK 465 ARG A 307 REMARK 465 GLU A 308 REMARK 465 GLY A 309 REMARK 465 ARG A 310 REMARK 465 GLU A 311 REMARK 465 PRO A 312 REMARK 465 CYS A 313 REMARK 465 GLU A 314 REMARK 465 LEU A 315 REMARK 465 SER A 576 REMARK 465 SER A 577 REMARK 465 GLN A 578 REMARK 465 TRP A 579 REMARK 465 VAL A 580 REMARK 465 ALA A 581 REMARK 465 GLY A 582 REMARK 465 GLU A 583 REMARK 465 GLN A 584 REMARK 465 GLN A 585 REMARK 465 VAL A 586 REMARK 465 SER B 1 REMARK 465 ASP B 2 REMARK 465 ALA B 108 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 166 CG CD OE1 OE2 REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 ILE A 297 CD1 REMARK 470 ARG A 318 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 571 CG CD OE1 NE2 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 64 -73.71 -110.71 REMARK 500 HIS A 99 50.87 -103.07 REMARK 500 ASP A 156 -95.46 10.45 REMARK 500 LYS A 268 116.79 -160.42 REMARK 500 PRO A 284 -17.48 -44.43 REMARK 500 ASP A 358 45.38 -77.66 REMARK 500 LYS A 359 4.81 -157.59 REMARK 500 ALA A 400 -39.36 -140.75 REMARK 500 LEU A 479 -70.60 -39.12 REMARK 500 ALA A 543 -159.19 -147.76 REMARK 500 THR A 559 74.92 -154.59 REMARK 500 VAL A 652 76.06 -112.19 REMARK 500 HIS A 653 -77.07 66.21 REMARK 500 ASP B 20 88.66 28.61 REMARK 500 GLN B 50 100.68 -55.54 REMARK 500 ALA B 88 147.11 -174.35 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 DC P 20 0.08 SIDE CHAIN REMARK 500 DG T 7 0.06 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 A4003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 5 OD1 REMARK 620 2 HOH A5031 O 70.9 REMARK 620 3 HOH A5044 O 72.2 78.4 REMARK 620 4 HOH A5432 O 82.4 152.0 85.7 REMARK 620 5 HOH A5433 O 77.8 79.5 147.2 103.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A4001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 475 OD1 REMARK 620 2 ALA A 476 O 90.2 REMARK 620 3 ASP A 654 OD2 78.3 88.4 REMARK 620 4 DAD A4004 O1G 109.8 99.9 168.1 REMARK 620 5 DAD A4004 O2B 163.0 85.9 85.0 87.2 REMARK 620 6 DAD A4004 O1A 103.6 160.2 80.8 88.7 76.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A4002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 475 OD1 REMARK 620 2 ASP A 475 OD2 44.2 REMARK 620 3 ASP A 654 OD1 66.0 108.7 REMARK 620 4 DAD A4004 O1A 76.1 95.1 78.1 REMARK 620 5 HOH A5017 O 126.9 115.4 92.8 149.4 REMARK 620 6 HOH A5442 O 131.4 94.7 152.3 85.6 90.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 4002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 4003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAD A 4004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T7P RELATED DB: PDB REMARK 900 T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE, A NUCLEOSIDE REMARK 900 TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN REMARK 900 RELATED ID: 1SKS RELATED DB: PDB REMARK 900 BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE REMARK 900 CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE REMARK 900 RELATED ID: 1SKW RELATED DB: PDB REMARK 900 BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE REMARK 900 CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON THE TEMPLATE REMARK 900 RELATED ID: 1SL0 RELATED DB: PDB REMARK 900 TERNARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE REMARK 900 CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON THE TEMPLATE AND REMARK 900 AN INCOMING NUCLEOTIDE REMARK 900 RELATED ID: 1SL1 RELATED DB: PDB REMARK 900 BINARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE REMARK 900 CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE REMARK 900 RELATED ID: 1SL2 RELATED DB: PDB REMARK 900 TERNARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE REMARK 900 CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE AND AN INCOMING REMARK 900 NUCLEOTIDE DBREF 1SKR A 1 704 UNP P00581 DPOL_BPT7 1 704 DBREF 1SKR B 1 108 UNP P0AA25 THIO_ECOLI 1 108 DBREF 1SKR P 1 22 PDB 1SKR 1SKR 1 22 DBREF 1SKR T 1 26 PDB 1SKR 1SKR 1 26 SEQADV 1SKR A UNP P00581 LYS 118 DELETION SEQADV 1SKR A UNP P00581 ARG 119 DELETION SEQADV 1SKR A UNP P00581 PHE 120 DELETION SEQADV 1SKR A UNP P00581 GLY 121 DELETION SEQADV 1SKR A UNP P00581 SER 122 DELETION SEQADV 1SKR A UNP P00581 HIS 123 DELETION SEQRES 1 P 22 DC DG DA DA DA DA DC DG DA DC DG DG DC SEQRES 2 P 22 DC DA DG DT DG DC DC DA 2DA SEQRES 1 T 26 DC DC DC DT DT DT DG DG DC DA DC DT DG SEQRES 2 T 26 DG DC DC DG DT DC DG DT DT DT DT DC DG SEQRES 1 A 698 MET ILE VAL SER ASP ILE GLU ALA ASN ALA LEU LEU GLU SEQRES 2 A 698 SER VAL THR LYS PHE HIS CYS GLY VAL ILE TYR ASP TYR SEQRES 3 A 698 SER THR ALA GLU TYR VAL SER TYR ARG PRO SER ASP PHE SEQRES 4 A 698 GLY ALA TYR LEU ASP ALA LEU GLU ALA GLU VAL ALA ARG SEQRES 5 A 698 GLY GLY LEU ILE VAL PHE HIS ASN GLY HIS LYS TYR ASP SEQRES 6 A 698 VAL PRO ALA LEU THR LYS LEU ALA LYS LEU GLN LEU ASN SEQRES 7 A 698 ARG GLU PHE HIS LEU PRO ARG GLU ASN CYS ILE ASP THR SEQRES 8 A 698 LEU VAL LEU SER ARG LEU ILE HIS SER ASN LEU LYS ASP SEQRES 9 A 698 THR ASP MET GLY LEU LEU ARG SER GLY LYS LEU PRO GLY SEQRES 10 A 698 ALA LEU GLU ALA TRP GLY TYR ARG LEU GLY GLU MET LYS SEQRES 11 A 698 GLY GLU TYR LYS ASP ASP PHE LYS ARG MET LEU GLU GLU SEQRES 12 A 698 GLN GLY GLU GLU TYR VAL ASP GLY MET GLU TRP TRP ASN SEQRES 13 A 698 PHE ASN GLU GLU MET MET ASP TYR ASN VAL GLN ASP VAL SEQRES 14 A 698 VAL VAL THR LYS ALA LEU LEU GLU LYS LEU LEU SER ASP SEQRES 15 A 698 LYS HIS TYR PHE PRO PRO GLU ILE ASP PHE THR ASP VAL SEQRES 16 A 698 GLY TYR THR THR PHE TRP SER GLU SER LEU GLU ALA VAL SEQRES 17 A 698 ASP ILE GLU HIS ARG ALA ALA TRP LEU LEU ALA LYS GLN SEQRES 18 A 698 GLU ARG ASN GLY PHE PRO PHE ASP THR LYS ALA ILE GLU SEQRES 19 A 698 GLU LEU TYR VAL GLU LEU ALA ALA ARG ARG SER GLU LEU SEQRES 20 A 698 LEU ARG LYS LEU THR GLU THR PHE GLY SER TRP TYR GLN SEQRES 21 A 698 PRO LYS GLY GLY THR GLU MET PHE CYS HIS PRO ARG THR SEQRES 22 A 698 GLY LYS PRO LEU PRO LYS TYR PRO ARG ILE LYS THR PRO SEQRES 23 A 698 LYS VAL GLY GLY ILE PHE LYS LYS PRO LYS ASN LYS ALA SEQRES 24 A 698 GLN ARG GLU GLY ARG GLU PRO CYS GLU LEU ASP THR ARG SEQRES 25 A 698 GLU TYR VAL ALA GLY ALA PRO TYR THR PRO VAL GLU HIS SEQRES 26 A 698 VAL VAL PHE ASN PRO SER SER ARG ASP HIS ILE GLN LYS SEQRES 27 A 698 LYS LEU GLN GLU ALA GLY TRP VAL PRO THR LYS TYR THR SEQRES 28 A 698 ASP LYS GLY ALA PRO VAL VAL ASP ASP GLU VAL LEU GLU SEQRES 29 A 698 GLY VAL ARG VAL ASP ASP PRO GLU LYS GLN ALA ALA ILE SEQRES 30 A 698 ASP LEU ILE LYS GLU TYR LEU MET ILE GLN LYS ARG ILE SEQRES 31 A 698 GLY GLN SER ALA GLU GLY ASP LYS ALA TRP LEU ARG TYR SEQRES 32 A 698 VAL ALA GLU ASP GLY LYS ILE HIS GLY SER VAL ASN PRO SEQRES 33 A 698 ASN GLY ALA VAL THR GLY ARG ALA THR HIS ALA PHE PRO SEQRES 34 A 698 ASN LEU ALA GLN ILE PRO GLY VAL ARG SER PRO TYR GLY SEQRES 35 A 698 GLU GLN CYS ARG ALA ALA PHE GLY ALA GLU HIS HIS LEU SEQRES 36 A 698 ASP GLY ILE THR GLY LYS PRO TRP VAL GLN ALA GLY ILE SEQRES 37 A 698 ASP ALA SER GLY LEU GLU LEU ARG CYS LEU ALA HIS PHE SEQRES 38 A 698 MET ALA ARG PHE ASP ASN GLY GLU TYR ALA HIS GLU ILE SEQRES 39 A 698 LEU ASN GLY ASP ILE HIS THR LYS ASN GLN ILE ALA ALA SEQRES 40 A 698 GLU LEU PRO THR ARG ASP ASN ALA LYS THR PHE ILE TYR SEQRES 41 A 698 GLY PHE LEU TYR GLY ALA GLY ASP GLU LYS ILE GLY GLN SEQRES 42 A 698 ILE VAL GLY ALA GLY LYS GLU ARG GLY LYS GLU LEU LYS SEQRES 43 A 698 LYS LYS PHE LEU GLU ASN THR PRO ALA ILE ALA ALA LEU SEQRES 44 A 698 ARG GLU SER ILE GLN GLN THR LEU VAL GLU SER SER GLN SEQRES 45 A 698 TRP VAL ALA GLY GLU GLN GLN VAL LYS TRP LYS ARG ARG SEQRES 46 A 698 TRP ILE LYS GLY LEU ASP GLY ARG LYS VAL HIS VAL ARG SEQRES 47 A 698 SER PRO HIS ALA ALA LEU ASN THR LEU LEU GLN SER ALA SEQRES 48 A 698 GLY ALA LEU ILE CYS LYS LEU TRP ILE ILE LYS THR GLU SEQRES 49 A 698 GLU MET LEU VAL GLU LYS GLY LEU LYS HIS GLY TRP ASP SEQRES 50 A 698 GLY ASP PHE ALA TYR MET ALA TRP VAL HIS ASP GLU ILE SEQRES 51 A 698 GLN VAL GLY CYS ARG THR GLU GLU ILE ALA GLN VAL VAL SEQRES 52 A 698 ILE GLU THR ALA GLN GLU ALA MET ARG TRP VAL GLY ASP SEQRES 53 A 698 HIS TRP ASN PHE ARG CYS LEU LEU ASP THR GLU GLY LYS SEQRES 54 A 698 MET GLY PRO ASN TRP ALA ILE CYS HIS SEQRES 1 B 108 SER ASP LYS ILE ILE HIS LEU THR ASP ASP SER PHE ASP SEQRES 2 B 108 THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL ASP SEQRES 3 B 108 PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS MET ILE ALA SEQRES 4 B 108 PRO ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY LYS SEQRES 5 B 108 LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO GLY SEQRES 6 B 108 THR ALA PRO LYS TYR GLY ILE ARG GLY ILE PRO THR LEU SEQRES 7 B 108 LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS VAL SEQRES 8 B 108 GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU ASP SEQRES 9 B 108 ALA ASN LEU ALA MODRES 1SKR 2DA P 22 DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HET 2DA P 22 20 HET MG A4001 1 HET MG A4002 1 HET MG A4003 1 HET DAD A4004 29 HETNAM 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE FORMUL 1 2DA C10 H14 N5 O5 P FORMUL 5 MG 3(MG 2+) FORMUL 8 DAD C10 H16 N5 O11 P3 FORMUL 9 HOH *381(H2 O) HELIX 1 1 ARG A 35 SER A 37 5 3 HELIX 2 2 ASP A 38 ARG A 52 1 15 HELIX 3 3 TYR A 64 ASN A 78 1 15 HELIX 4 4 PRO A 84 GLU A 86 5 3 HELIX 5 5 THR A 91 HIS A 99 1 9 HELIX 6 6 ARG A 111 LEU A 115 5 5 HELIX 7 7 GLU A 126 GLU A 149 1 24 HELIX 8 8 GLY A 157 TRP A 161 5 5 HELIX 9 9 ASN A 164 SER A 187 1 24 HELIX 10 10 GLY A 202 SER A 210 1 9 HELIX 11 11 LEU A 211 GLY A 231 1 21 HELIX 12 12 ASP A 235 PHE A 261 1 27 HELIX 13 13 SER A 338 GLU A 348 1 11 HELIX 14 14 ASP A 365 VAL A 372 1 8 HELIX 15 15 ASP A 376 ALA A 400 1 25 HELIX 16 16 ALA A 405 VAL A 410 1 6 HELIX 17 17 ASN A 436 ILE A 440 5 5 HELIX 18 18 TYR A 447 ALA A 454 1 8 HELIX 19 19 PHE A 455 PHE A 455 5 1 HELIX 20 20 GLY A 456 HIS A 460 5 5 HELIX 21 21 GLY A 478 ASN A 493 1 16 HELIX 22 22 GLY A 494 ILE A 500 1 7 HELIX 23 23 ASP A 504 GLU A 514 1 11 HELIX 24 24 THR A 517 TYR A 530 1 14 HELIX 25 25 GLY A 533 GLY A 542 1 10 HELIX 26 26 GLY A 544 ASN A 558 1 15 HELIX 27 27 PRO A 560 VAL A 574 1 15 HELIX 28 28 SER A 605 HIS A 607 5 3 HELIX 29 29 ALA A 608 LYS A 636 1 29 HELIX 30 30 THR A 662 TRP A 684 1 23 HELIX 31 31 SER B 11 VAL B 16 1 6 HELIX 32 32 CYS B 32 TYR B 49 1 18 HELIX 33 33 THR B 66 GLY B 71 5 6 HELIX 34 34 SER B 95 LEU B 107 1 13 SHEET 1 A 5 GLU A 30 TYR A 34 0 SHEET 2 A 5 PHE A 18 ASP A 25 -1 N GLY A 21 O TYR A 34 SHEET 3 A 5 ILE A 2 ALA A 8 -1 N VAL A 3 O TYR A 24 SHEET 4 A 5 ILE A 56 PHE A 58 1 O VAL A 57 N ILE A 2 SHEET 5 A 5 CYS A 88 ASP A 90 1 O ILE A 89 N PHE A 58 SHEET 1 B 2 PHE A 232 PRO A 233 0 SHEET 2 B 2 LYS A 415 ILE A 416 -1 O ILE A 416 N PHE A 232 SHEET 1 C 3 TRP A 264 PRO A 267 0 SHEET 2 C 3 THR A 327 VAL A 332 -1 O VAL A 332 N TRP A 264 SHEET 3 C 3 GLY B 74 ILE B 75 -1 O ILE B 75 N THR A 327 SHEET 1 D 2 SER A 419 ASN A 421 0 SHEET 2 D 2 THR A 431 ALA A 433 -1 O ALA A 433 N SER A 419 SHEET 1 E 4 PHE A 646 TRP A 651 0 SHEET 2 E 4 GLU A 655 CYS A 660 -1 O GLY A 659 N ALA A 647 SHEET 3 E 4 VAL A 470 ALA A 476 -1 N VAL A 470 O CYS A 660 SHEET 4 E 4 THR A 692 GLY A 697 -1 O LYS A 695 N GLY A 473 SHEET 1 F 2 TRP A 592 LYS A 594 0 SHEET 2 F 2 LYS A 600 HIS A 602 -1 O VAL A 601 N ILE A 593 SHEET 1 G 5 ILE B 5 HIS B 6 0 SHEET 2 G 5 THR B 54 ASN B 59 1 O LYS B 57 N ILE B 5 SHEET 3 G 5 ALA B 22 TRP B 28 1 N LEU B 24 O THR B 54 SHEET 4 G 5 THR B 77 LYS B 82 -1 O LEU B 79 N VAL B 25 SHEET 5 G 5 GLU B 85 VAL B 91 -1 O LYS B 90 N LEU B 78 LINK O3' DA P 21 P 2DA P 22 1555 1555 1.61 LINK OD1 ASP A 5 MG MG A4003 1555 1555 2.57 LINK OD1 ASP A 475 MG MG A4001 1555 1555 2.25 LINK OD1 ASP A 475 MG MG A4002 1555 1555 3.12 LINK OD2 ASP A 475 MG MG A4002 1555 1555 2.47 LINK O ALA A 476 MG MG A4001 1555 1555 2.17 LINK OD2 ASP A 654 MG MG A4001 1555 1555 2.33 LINK OD1 ASP A 654 MG MG A4002 1555 1555 2.44 LINK MG MG A4001 O1G DAD A4004 1555 1555 2.28 LINK MG MG A4001 O2B DAD A4004 1555 1555 2.38 LINK MG MG A4001 O1A DAD A4004 1555 1555 2.34 LINK MG MG A4002 O1A DAD A4004 1555 1555 2.72 LINK MG MG A4002 O HOH A5017 1555 1555 2.55 LINK MG MG A4002 O HOH A5442 1555 1555 2.70 LINK MG MG A4003 O HOH A5031 1555 1555 2.49 LINK MG MG A4003 O HOH A5044 1555 1555 2.57 LINK MG MG A4003 O HOH A5432 1555 1555 2.39 LINK MG MG A4003 O HOH A5433 1555 1555 2.46 CISPEP 1 PHE A 434 PRO A 435 0 -0.64 CISPEP 2 ILE B 75 PRO B 76 0 0.28 SITE 1 AC1 4 ASP A 475 ALA A 476 ASP A 654 DAD A4004 SITE 1 AC2 6 ASP A 475 ASP A 654 DAD A4004 HOH A5017 SITE 2 AC2 6 HOH A5442 2DA P 22 SITE 1 AC3 5 ASP A 5 HOH A5031 HOH A5044 HOH A5432 SITE 2 AC3 5 HOH A5433 SITE 1 AC4 22 ARG A 429 ASP A 475 ALA A 476 SER A 477 SITE 2 AC4 22 GLY A 478 LEU A 479 GLU A 480 HIS A 506 SITE 3 AC4 22 ARG A 518 LYS A 522 TYR A 526 ASP A 654 SITE 4 AC4 22 MG A4001 MG A4002 HOH A5008 HOH A5055 SITE 5 AC4 22 HOH A5168 HOH A5251 HOH A5284 2DA P 22 SITE 6 AC4 22 DT T 4 DT T 5 CRYST1 105.506 214.020 52.036 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 0.009478 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019217 0.00000