HEADER TRANSFERASE/ELECTRON TRANSPORT/DNA 05-MAR-04 1SKW TITLE BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA TITLE 2 PRIMER/TEMPLATE CONTAINING A DISORDERED CIS-SYN THYMINE TITLE 3 DIMER ON THE TEMPLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP* COMPND 4 CP*(2DT))-3'; COMPND 5 CHAIN: P; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: DNA PRIMER; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*CP*CP*CP*(TTD) COMPND 10 P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP* COMPND 11 CP*G)-3'; COMPND 12 CHAIN: T; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: DNA TEMPLATE; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA POLYMERASE; COMPND 17 CHAIN: A; COMPND 18 SYNONYM: T7 DNA POLYMERASE; COMPND 19 EC: 2.7.7.7; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES; COMPND 22 MOL_ID: 4; COMPND 23 MOLECULE: THIOREDOXIN 1; COMPND 24 CHAIN: B; COMPND 25 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, FIDELITY, LESION BYPASS, THYMINE DIMER, KEYWDS 2 OPEN, CLOSE, TRANSFERASE/ELECTRON TRANSPORT/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,S.DUTTA,S.DOUBLIE,H.M.BDOUR,J.S.TAYLOR,T.ELLENBERGER REVDAT 3 24-FEB-09 1SKW 1 VERSN REVDAT 2 03-AUG-04 1SKW 1 JRNL AUTHOR REVDAT 1 06-JUL-04 1SKW 0 JRNL AUTH Y.LI,S.DUTTA,S.DOUBLIE,H.M.BDOUR,J.S.TAYLOR, JRNL AUTH 2 T.ELLENBERGER JRNL TITL NUCLEOTIDE INSERTION OPPOSITE A CIS-SYN THYMINE JRNL TITL 2 DIMER BY A REPLICATIVE DNA POLYMERASE FROM JRNL TITL 3 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 1 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 51467 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) : 0.239 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2539 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7592 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 331 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6008 REMARK 3 NUCLEIC ACID ATOMS : 368 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.95000 REMARK 3 B22 (A**2) : -0.83000 REMARK 3 B33 (A**2) : -2.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.84 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) : 1.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.240 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.910 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.300 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 29.77 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: THE TTD IS MISSING DUE TO DISORDER REMARK 3 AND IS COVALENTLY LINKED. REMARK 4 REMARK 4 1SKW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-04. REMARK 100 THE RCSB ID CODE IS RCSB021800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51467 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 24.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52100 REMARK 200 FOR SHELL : 2.600 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 (%): 60.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, PH REMARK 280 7.5 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 52.35900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 105.74650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.35900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 105.74650 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 DG P 12 REMARK 465 DC P 13 REMARK 465 DC T 2 REMARK 465 DC T 3 REMARK 465 DC T 4 REMARK 465 TTD T 5 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 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 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 LYS A 114 CG CD CE NZ REMARK 470 ASP A 156 CG OD1 OD2 REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 GLU A 259 CG CD OE1 OE2 REMARK 470 LYS A 268 CD CE NZ REMARK 470 LYS A 281 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 LYS A 299 CG CD CE NZ REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 ASN A 303 CG OD1 ND2 REMARK 470 GLU A 314 CG CD OE1 OE2 REMARK 470 THR A 317 OG1 CG2 REMARK 470 ARG A 318 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 359 CD CE NZ REMARK 470 ARG A 444 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 495 CG CD OE1 OE2 REMARK 470 THR A 507 OG1 CG2 REMARK 470 GLN A 510 CG CD OE1 NE2 REMARK 470 LEU A 515 CG CD1 CD2 REMARK 470 THR A 517 OG1 CG2 REMARK 470 THR A 523 OG1 CG2 REMARK 470 ASP A 534 O CG OD1 OD2 REMARK 470 GLU A 535 CG CD OE1 OE2 REMARK 470 LYS A 536 CG CD CE NZ REMARK 470 ILE A 537 CG1 CG2 CD1 REMARK 470 GLN A 539 CG CD OE1 NE2 REMARK 470 ILE A 540 CG1 CG2 CD1 REMARK 470 VAL A 541 CG1 CG2 REMARK 470 LYS A 545 CG CD CE NZ REMARK 470 GLU A 546 CG CD OE1 OE2 REMARK 470 ARG A 547 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 549 CG CD CE NZ REMARK 470 GLU A 550 CG CD OE1 OE2 REMARK 470 LEU A 551 CG CD1 CD2 REMARK 470 LYS A 552 CG CD CE NZ REMARK 470 LYS A 553 CG CD CE NZ REMARK 470 LYS A 554 CG CD CE NZ REMARK 470 LEU A 556 CG CD1 CD2 REMARK 470 GLU A 557 CG CD OE1 OE2 REMARK 470 ASN A 558 CG OD1 ND2 REMARK 470 GLN A 571 CG CD OE1 NE2 REMARK 470 LYS A 587 CG CD CE NZ REMARK 470 LYS A 589 CG CD CE NZ REMARK 470 GLU A 693 CG CD OE1 OE2 REMARK 470 LYS A 695 CG CD CE NZ REMARK 470 HIS A 704 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 18 CE NZ REMARK 470 ASP B 20 CG OD1 OD2 REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 LYS B 36 CE NZ REMARK 470 ARG B 73 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 82 CG CD CE NZ 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 ALA A 10 -179.76 -176.66 REMARK 500 TYR A 64 -78.29 -120.19 REMARK 500 HIS A 99 45.09 -107.89 REMARK 500 GLU A 148 22.66 -66.42 REMARK 500 ASP A 156 -84.73 8.58 REMARK 500 ARG A 278 -73.85 -77.03 REMARK 500 LYS A 302 66.76 -160.57 REMARK 500 ARG A 318 165.87 -43.39 REMARK 500 LYS A 359 1.82 -164.11 REMARK 500 ALA A 400 -39.64 -138.99 REMARK 500 ASN A 423 41.16 -145.52 REMARK 500 TYR A 447 -0.15 69.83 REMARK 500 GLU A 514 78.51 -59.75 REMARK 500 PRO A 516 -89.73 -60.56 REMARK 500 ALA A 532 124.42 -177.64 REMARK 500 GLU A 535 -77.83 -59.67 REMARK 500 ALA A 543 -158.22 -60.80 REMARK 500 GLU A 546 -84.83 -67.69 REMARK 500 ARG A 590 124.46 -170.13 REMARK 500 VAL A 652 74.96 -112.64 REMARK 500 HIS A 653 -72.96 69.92 REMARK 500 CYS A 703 41.45 -90.29 REMARK 500 VAL B 16 -62.02 -107.30 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 DG T 8 0.05 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 THERE IS A DD-ATP PRESENT IN THE CRYSTAL BUT REMARK 600 NO DENSITY FOR IT. 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 HOH A5203 O REMARK 620 2 HOH A5030 O 158.9 REMARK 620 3 HOH A5202 O 83.7 97.9 REMARK 620 4 ASP A 5 OD1 75.0 84.3 82.0 REMARK 620 5 HOH A5204 O 79.7 89.7 151.2 71.1 REMARK 620 6 HOH A5206 O 117.3 82.2 109.3 163.5 99.3 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 4003 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 REMARK 900 NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR REMARK 900 THIOREDOXIN REMARK 900 RELATED ID: 1SKR RELATED DB: PDB REMARK 900 T7 DNA POLYMERASE COMPLEXED PRIMER/TEMPLATE DNA CONTAINING REMARK 900 A CIS-SYN THYMINE DIMER ON THE TEMPLATE REMARK 900 RELATED ID: 1SKS RELATED DB: PDB REMARK 900 BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ REMARK 900 TEMPLATE CONTAINING A 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/ REMARK 900 TEMPLATE CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON REMARK 900 THE TEMPLATE AND AN INCOMING NUCLEOTIDE REMARK 900 RELATED ID: 1SL1 RELATED DB: PDB REMARK 900 BINARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ REMARK 900 TEMPLATE 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/ REMARK 900 TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE REMARK 900 AND AN INCOMING NUCLEOTIDE DBREF 1SKW A 1 704 UNP P00581 DPOL_BPT7 1 704 DBREF 1SKW B 1 108 UNP P0AA25 THIO_ECOLI 1 108 DBREF 1SKW P 1 21 PDB 1SKW 1SKW 1 21 DBREF 1SKW T 2 26 PDB 1SKW 1SKW 2 26 SEQADV 1SKW A UNP P00581 LYS 118 DELETION SEQADV 1SKW A UNP P00581 ARG 119 DELETION SEQADV 1SKW A UNP P00581 PHE 120 DELETION SEQADV 1SKW A UNP P00581 GLY 121 DELETION SEQADV 1SKW A UNP P00581 SER 122 DELETION SEQADV 1SKW A UNP P00581 HIS 123 DELETION SEQRES 1 P 21 DC DG DA DA DA DA DC DG DA DC DG DG DC SEQRES 2 P 21 DC DA DG DT DG DC DC 2DT SEQRES 1 T 25 DC DC DC TTD DA DG DG DC DA DC DT DG DG SEQRES 2 T 25 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 1SKW 2DT P 21 DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE HET 2DT P 21 19 HET MG A4003 1 HETNAM 2DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN 2DT 2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE FORMUL 1 2DT C10 H15 N2 O7 P FORMUL 5 MG MG 2+ FORMUL 6 HOH *201(H2 O) HELIX 1 1 LEU A 11 VAL A 15 5 5 HELIX 2 2 ARG A 35 SER A 37 5 3 HELIX 3 3 ASP A 38 ARG A 52 1 15 HELIX 4 4 TYR A 64 ASN A 78 1 15 HELIX 5 5 PRO A 84 GLU A 86 5 3 HELIX 6 6 THR A 91 HIS A 99 1 9 HELIX 7 7 ARG A 111 LEU A 115 5 5 HELIX 8 8 GLU A 126 GLU A 148 1 23 HELIX 9 9 GLY A 157 TRP A 161 5 5 HELIX 10 10 ASN A 164 SER A 187 1 24 HELIX 11 11 GLY A 202 SER A 210 1 9 HELIX 12 12 LEU A 211 GLY A 231 1 21 HELIX 13 13 ASP A 235 PHE A 261 1 27 HELIX 14 14 SER A 338 GLU A 348 1 11 HELIX 15 15 ASP A 365 VAL A 372 1 8 HELIX 16 16 ASP A 376 ALA A 400 1 25 HELIX 17 17 ALA A 405 VAL A 410 1 6 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 ASN A 502 1 9 HELIX 23 23 ASP A 504 ALA A 513 1 10 HELIX 24 24 THR A 517 TYR A 530 1 14 HELIX 25 25 ILE A 537 VAL A 541 5 5 HELIX 26 26 GLY A 544 THR A 559 1 16 HELIX 27 27 THR A 559 VAL A 574 1 16 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 TYR A 31 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 GLU A 7 O CYS A 20 SHEET 4 A 5 ILE A 56 PHE A 58 1 O VAL A 57 N SER A 4 SHEET 5 A 5 CYS A 88 ASP A 90 1 O ILE A 89 N ILE A 56 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 GLU A 330 N GLN A 266 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 THR A 431 N ASN A 421 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 GLY A 697 N GLN A 471 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 LEU B 53 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 ALA B 56 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 MG MG A4003 O HOH A5203 1555 1555 2.44 LINK MG MG A4003 O HOH A5030 1555 1555 2.60 LINK MG MG A4003 O HOH A5202 1555 1555 2.36 LINK MG MG A4003 OD1 ASP A 5 1555 1555 2.45 LINK MG MG A4003 O HOH A5204 1555 1555 2.46 LINK MG MG A4003 O HOH A5206 1555 1555 2.52 LINK O3' DC P 20 P 2DT P 21 1555 1555 1.61 CISPEP 1 PHE A 434 PRO A 435 0 -0.56 CISPEP 2 ILE B 75 PRO B 76 0 0.05 SITE 1 AC1 6 ASP A 5 HOH A5030 HOH A5202 HOH A5203 SITE 2 AC1 6 HOH A5204 HOH A5206 CRYST1 104.718 211.493 52.187 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 0.009549 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019162 0.00000