HEADER TRANSFERASE/DNA 19-APR-13 4K8X TITLE BINARY COMPLEX OF 9N DNA POLYMERASE IN THE REPLICATIVE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*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 (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA PRIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS; SOURCE 3 ORGANISM_TAXID: 103799; SOURCE 4 STRAIN: 9ON-7; SOURCE 5 GENE: POL, POLA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA POLYMERASE, BINARY COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,K.DIEDERICHS,A.MARX REVDAT 2 08-NOV-23 4K8X 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK REVDAT 1 26-JUN-13 4K8X 0 JRNL AUTH K.BERGEN,K.BETZ,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL STRUCTURES OF KOD AND 9N DNA POLYMERASES COMPLEXED WITH JRNL TITL 2 PRIMER TEMPLATE DUPLEX JRNL REF CHEMBIOCHEM V. 14 1058 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 23733496 JRNL DOI 10.1002/CBIC.201300175 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1345) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49542 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2524 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.7235 - 5.9718 1.00 2803 164 0.1630 0.1824 REMARK 3 2 5.9718 - 4.7413 1.00 2677 152 0.1463 0.1971 REMARK 3 3 4.7413 - 4.1423 1.00 2644 140 0.1224 0.1538 REMARK 3 4 4.1423 - 3.7637 1.00 2650 139 0.1468 0.1632 REMARK 3 5 3.7637 - 3.4941 0.99 2600 138 0.1785 0.2346 REMARK 3 6 3.4941 - 3.2881 1.00 2632 134 0.1861 0.2531 REMARK 3 7 3.2881 - 3.1235 1.00 2607 135 0.2139 0.2928 REMARK 3 8 3.1235 - 2.9875 1.00 2598 144 0.2463 0.3240 REMARK 3 9 2.9875 - 2.8725 1.00 2586 151 0.2547 0.3251 REMARK 3 10 2.8725 - 2.7734 1.00 2600 117 0.2498 0.3340 REMARK 3 11 2.7734 - 2.6867 1.00 2581 135 0.2584 0.3217 REMARK 3 12 2.6867 - 2.6099 1.00 2559 161 0.2652 0.2884 REMARK 3 13 2.6099 - 2.5412 1.00 2582 133 0.2647 0.2782 REMARK 3 14 2.5412 - 2.4792 1.00 2565 143 0.2867 0.3761 REMARK 3 15 2.4792 - 2.4228 1.00 2584 136 0.3042 0.3581 REMARK 3 16 2.4228 - 2.3713 1.00 2584 143 0.3288 0.3983 REMARK 3 17 2.3713 - 2.3239 1.00 2563 133 0.3483 0.3854 REMARK 3 18 2.3239 - 2.2800 1.00 2603 126 0.3660 0.4217 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.70 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 7194 REMARK 3 ANGLE : 1.157 9849 REMARK 3 CHIRALITY : 0.072 1035 REMARK 3 PLANARITY : 0.005 1196 REMARK 3 DIHEDRAL : 17.718 2826 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1:123) REMARK 3 ORIGIN FOR THE GROUP (A): -32.1449 39.1512 -40.3743 REMARK 3 T TENSOR REMARK 3 T11: 0.2563 T22: 0.5963 REMARK 3 T33: 0.5609 T12: -0.0399 REMARK 3 T13: -0.0449 T23: 0.1724 REMARK 3 L TENSOR REMARK 3 L11: 3.6473 L22: 1.3190 REMARK 3 L33: 3.8282 L12: -0.4046 REMARK 3 L13: -0.2006 L23: 0.7105 REMARK 3 S TENSOR REMARK 3 S11: 0.0206 S12: 0.9207 S13: 0.2682 REMARK 3 S21: -0.2214 S22: -0.0341 S23: 0.1697 REMARK 3 S31: -0.0939 S32: -0.1826 S33: 0.0241 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 124:255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -51.4269 29.5190 -12.1571 REMARK 3 T TENSOR REMARK 3 T11: 0.2457 T22: 0.5913 REMARK 3 T33: 0.4435 T12: 0.0160 REMARK 3 T13: -0.0002 T23: -0.1157 REMARK 3 L TENSOR REMARK 3 L11: 5.4308 L22: 2.4759 REMARK 3 L33: 3.0655 L12: 1.8564 REMARK 3 L13: -2.5032 L23: -1.4693 REMARK 3 S TENSOR REMARK 3 S11: -0.1672 S12: 0.4184 S13: -0.3282 REMARK 3 S21: 0.0020 S22: 0.1008 S23: 0.0816 REMARK 3 S31: 0.0990 S32: -0.6809 S33: 0.0509 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 256:553 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4288 24.2237 -14.4604 REMARK 3 T TENSOR REMARK 3 T11: 0.2627 T22: 0.3301 REMARK 3 T33: 0.3865 T12: -0.0190 REMARK 3 T13: -0.0220 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 2.0972 L22: 0.9676 REMARK 3 L33: 0.6157 L12: -0.2433 REMARK 3 L13: 0.0822 L23: 0.0311 REMARK 3 S TENSOR REMARK 3 S11: -0.0440 S12: -0.0959 S13: -0.1525 REMARK 3 S21: 0.1334 S22: -0.0222 S23: -0.0982 REMARK 3 S31: 0.0849 S32: 0.0728 S33: 0.0644 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 554:758 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.0868 2.8494 -1.5516 REMARK 3 T TENSOR REMARK 3 T11: 0.4583 T22: 0.5024 REMARK 3 T33: 0.8710 T12: 0.0193 REMARK 3 T13: 0.0860 T23: 0.1176 REMARK 3 L TENSOR REMARK 3 L11: 3.8353 L22: 1.7817 REMARK 3 L33: 1.5605 L12: 0.4740 REMARK 3 L13: 0.8128 L23: -0.0560 REMARK 3 S TENSOR REMARK 3 S11: 0.1827 S12: -0.4446 S13: -0.9885 REMARK 3 S21: 0.3309 S22: 0.0181 S23: 0.2633 REMARK 3 S31: 0.2539 S32: -0.2910 S33: -0.1652 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESSEQ 1:16) REMARK 3 ORIGIN FOR THE GROUP (A): -22.3139 4.9457 -16.3651 REMARK 3 T TENSOR REMARK 3 T11: 0.3951 T22: 0.5226 REMARK 3 T33: 1.0002 T12: -0.0482 REMARK 3 T13: 0.0619 T23: -0.0743 REMARK 3 L TENSOR REMARK 3 L11: 1.7468 L22: 0.3294 REMARK 3 L33: 2.2371 L12: 0.3200 REMARK 3 L13: 0.7472 L23: -0.2102 REMARK 3 S TENSOR REMARK 3 S11: 0.1601 S12: 0.3177 S13: -0.9959 REMARK 3 S21: -0.2326 S22: -0.3728 S23: 0.3475 REMARK 3 S31: 0.3333 S32: -0.1484 S33: 0.2298 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESSEQ 1:11) REMARK 3 ORIGIN FOR THE GROUP (A): -22.7619 -3.1801 -17.2415 REMARK 3 T TENSOR REMARK 3 T11: 0.6738 T22: 0.5691 REMARK 3 T33: 1.5930 T12: -0.0309 REMARK 3 T13: 0.0153 T23: -0.1558 REMARK 3 L TENSOR REMARK 3 L11: 0.2381 L22: 4.7352 REMARK 3 L33: 2.1501 L12: -0.9648 REMARK 3 L13: 0.2965 L23: -2.3681 REMARK 3 S TENSOR REMARK 3 S11: 0.5751 S12: 0.3973 S13: -1.6466 REMARK 3 S21: -0.5994 S22: -0.2244 S23: -0.7420 REMARK 3 S31: 0.8849 S32: -0.1494 S33: -0.3725 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4K8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97793 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49600 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 48.712 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1QHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM CHLORIDE, 2.2M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 56.10750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 71.30800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 56.10750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 71.30800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -158.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 THR A 760 REMARK 465 LYS A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 GLY A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 VAL A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 LYS A 774 REMARK 465 LYS A 775 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 T 2 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG T 4 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC T 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG T 10 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG T 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC T 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG P 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC P 10 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DC P 10 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DOC P 12 O3' - P - O5' ANGL. DEV. = -21.1 DEGREES REMARK 500 DOC P 12 O3' - P - OP2 ANGL. DEV. = 18.1 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 SER A 301 15.68 -142.97 REMARK 500 GLU A 303 -113.83 -72.50 REMARK 500 ASN A 399 71.82 56.88 REMARK 500 GLU A 436 -59.84 60.20 REMARK 500 TRP A 504 40.04 -95.51 REMARK 500 THR A 541 -67.93 69.83 REMARK 500 LYS A 592 -7.67 73.75 REMARK 500 GLN A 736 -74.52 -115.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5CY T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO T 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QHT RELATED DB: PDB REMARK 900 APO STRUCTURE OF 9 N DNA POLYMERASE REMARK 900 RELATED ID: 4K8Z RELATED DB: PDB DBREF 4K8X A 1 775 UNP Q56366 DPOL_THES9 1 775 DBREF 4K8X T 1 16 PDB 4K8X 4K8X 1 16 DBREF 4K8X P 1 12 PDB 4K8X 4K8X 1 12 SEQADV 4K8X ALA A 141 UNP Q56366 ASP 141 ENGINEERED MUTATION SEQADV 4K8X ALA A 143 UNP Q56366 GLU 143 ENGINEERED MUTATION SEQRES 1 A 775 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASN GLY LYS SEQRES 2 A 775 PRO VAL ILE ARG VAL PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 775 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 775 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU ASP VAL LYS SEQRES 5 A 775 LYS VAL THR ALA LYS ARG HIS GLY THR VAL VAL LYS VAL SEQRES 6 A 775 LYS ARG ALA GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 775 PRO ILE GLU VAL TRP LYS LEU TYR PHE ASN HIS PRO GLN SEQRES 8 A 775 ASP VAL PRO ALA ILE ARG ASP ARG ILE ARG ALA HIS PRO SEQRES 9 A 775 ALA VAL VAL ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 775 LYS ARG TYR LEU ILE ASP LYS GLY LEU ILE PRO MET GLU SEQRES 11 A 775 GLY ASP GLU GLU LEU THR MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 775 THR LEU TYR HIS GLU GLY GLU GLU PHE GLY THR GLY PRO SEQRES 13 A 775 ILE LEU MET ILE SER TYR ALA ASP GLY SER GLU ALA ARG SEQRES 14 A 775 VAL ILE THR TRP LYS LYS ILE ASP LEU PRO TYR VAL ASP SEQRES 15 A 775 VAL VAL SER THR GLU LYS GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 775 ARG VAL VAL ARG GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 775 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 775 ARG CYS GLU GLU LEU GLY ILE LYS PHE THR LEU GLY ARG SEQRES 19 A 775 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 775 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 775 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 775 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY LYS PRO SEQRES 23 A 775 LYS GLU LYS VAL TYR ALA GLU GLU ILE ALA GLN ALA TRP SEQRES 24 A 775 GLU SER GLY GLU GLY LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 775 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY ARG GLU SEQRES 26 A 775 PHE PHE PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 775 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 775 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR LYS ARG SEQRES 29 A 775 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU ARG GLU LEU SEQRES 30 A 775 ALA ARG ARG ARG GLY GLY TYR ALA GLY GLY TYR VAL LYS SEQRES 31 A 775 GLU PRO GLU ARG GLY LEU TRP ASP ASN ILE VAL TYR LEU SEQRES 32 A 775 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 775 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS LYS SEQRES 34 A 775 GLU TYR ASP VAL ALA PRO GLU VAL GLY HIS LYS PHE CYS SEQRES 35 A 775 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 775 LEU LEU GLU GLU ARG GLN LYS ILE LYS ARG LYS MET LYS SEQRES 37 A 775 ALA THR VAL ASP PRO LEU GLU LYS LYS LEU LEU ASP TYR SEQRES 38 A 775 ARG GLN ARG ALA ILE LYS ILE LEU ALA ASN SER PHE TYR SEQRES 39 A 775 GLY TYR TYR GLY TYR ALA LYS ALA ARG TRP TYR CYS LYS SEQRES 40 A 775 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 775 ILE GLU MET VAL ILE ARG GLU LEU GLU GLU LYS PHE GLY SEQRES 42 A 775 PHE LYS VAL LEU TYR ALA ASP THR ASP GLY LEU HIS ALA SEQRES 43 A 775 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 775 ALA LYS GLU PHE LEU LYS TYR ILE ASN PRO LYS LEU PRO SEQRES 45 A 775 GLY LEU LEU GLU LEU GLU TYR GLU GLY PHE TYR VAL ARG SEQRES 46 A 775 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 775 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 775 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 775 ARG VAL LEU GLU ALA ILE LEU LYS HIS GLY ASP VAL GLU SEQRES 50 A 775 GLU ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 775 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 775 GLU GLN ILE THR ARG ASP LEU ARG ASP TYR LYS ALA THR SEQRES 53 A 775 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 775 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 775 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 775 PRO ALA ASP GLU PHE ASP PRO THR LYS HIS ARG TYR ASP SEQRES 57 A 775 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 775 GLU ARG ILE LEU LYS ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 775 LEU ARG TYR GLN LYS THR LYS GLN VAL GLY LEU GLY ALA SEQRES 60 A 775 TRP LEU LYS VAL LYS GLY LYS LYS SEQRES 1 T 16 DA DA DA DG DG DC DG DC DA DG DT DT DC SEQRES 2 T 16 DG DC DG SEQRES 1 P 12 DC DG DC DG DA DA DC DT DG DC DG DOC MODRES 4K8X DOC P 12 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC P 12 18 HET SO4 A 801 5 HET SO4 A 802 5 HET SO4 A 803 5 HET SO4 A 804 5 HET SO4 A 805 5 HET SO4 A 806 5 HET SO4 A 807 5 HET SO4 A 808 5 HET SO4 A 809 5 HET CL A 810 1 HET SO4 A 811 5 HET SO4 A 812 5 HET 5CY T 101 70 HET EDO T 102 4 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM 5CY 1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3- HETNAM 2 5CY HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2- HETNAM 3 5CY YLIDENE]PENTA-1,3-DIEN-1-Y L}-3,3-DIMETHYL-3H-INDOLIUM HETNAM EDO 1,2-ETHANEDIOL HETSYN 5CY N,N'-(DIPROPYL)-TETRAMETHYLINDODICARBOCYANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 DOC C9 H14 N3 O6 P FORMUL 4 SO4 11(O4 S 2-) FORMUL 13 CL CL 1- FORMUL 16 5CY C31 H39 N2 O2 1+ FORMUL 17 EDO C2 H6 O2 FORMUL 18 HOH *134(H2 O) HELIX 1 1 ASP A 44 SER A 46 5 3 HELIX 2 2 ALA A 47 LYS A 53 1 7 HELIX 3 3 GLN A 91 HIS A 103 1 13 HELIX 4 4 PRO A 115 LYS A 124 1 10 HELIX 5 5 THR A 186 ASP A 202 1 17 HELIX 6 6 PHE A 214 LEU A 226 1 13 HELIX 7 7 LEU A 260 ILE A 268 1 9 HELIX 8 8 THR A 274 GLY A 284 1 11 HELIX 9 9 TYR A 291 GLY A 302 1 12 HELIX 10 10 GLY A 304 GLY A 338 1 35 HELIX 11 11 SER A 340 SER A 345 1 6 HELIX 12 12 SER A 348 ARG A 364 1 17 HELIX 13 13 ASP A 373 ARG A 379 1 7 HELIX 14 14 SER A 407 HIS A 416 1 10 HELIX 15 15 GLY A 447 THR A 470 1 24 HELIX 16 16 ASP A 472 ASN A 491 1 20 HELIX 17 17 SER A 492 GLY A 498 1 7 HELIX 18 18 CYS A 506 LYS A 531 1 26 HELIX 19 19 ASP A 552 ASN A 568 1 17 HELIX 20 20 PRO A 569 LEU A 571 5 3 HELIX 21 21 LEU A 608 ARG A 612 5 5 HELIX 22 22 SER A 616 HIS A 633 1 18 HELIX 23 23 ASP A 635 LYS A 652 1 18 HELIX 24 24 PRO A 656 VAL A 661 5 6 HELIX 25 25 ASP A 669 TYR A 673 5 5 HELIX 26 26 GLY A 677 GLY A 690 1 14 HELIX 27 27 ARG A 709 ASP A 712 5 4 HELIX 28 28 ASP A 718 PHE A 720 5 3 HELIX 29 29 ASP A 728 ASN A 735 1 8 HELIX 30 30 GLN A 736 LYS A 746 1 11 HELIX 31 31 ALA A 747 GLY A 749 5 3 HELIX 32 32 LYS A 752 ARG A 756 5 5 SHEET 1 A 3 ILE A 2 GLU A 10 0 SHEET 2 A 3 LYS A 13 GLU A 22 -1 O PHE A 19 N LEU A 3 SHEET 3 A 3 GLU A 25 ASP A 31 -1 O LYS A 27 N LYS A 20 SHEET 1 B 4 ARG A 67 PHE A 75 0 SHEET 2 B 4 ARG A 78 TYR A 86 -1 O ILE A 80 N LYS A 73 SHEET 3 B 4 TYR A 37 LEU A 42 -1 N PHE A 38 O LEU A 85 SHEET 4 B 4 VAL A 106 TYR A 110 -1 O ASP A 108 N LEU A 41 SHEET 1 C 2 THR A 55 ARG A 58 0 SHEET 2 C 2 THR A 61 LYS A 64 -1 O THR A 61 N ARG A 58 SHEET 1 D 6 VAL A 181 VAL A 183 0 SHEET 2 D 6 ALA A 168 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 D 6 ILE A 157 ALA A 163 -1 N ILE A 160 O ILE A 171 SHEET 4 D 6 MET A 137 THR A 144 -1 N ALA A 139 O ALA A 163 SHEET 5 D 6 VAL A 205 THR A 208 1 O ILE A 207 N LEU A 138 SHEET 6 D 6 ILE A 256 ASP A 259 1 O ILE A 256 N LEU A 206 SHEET 1 E 2 LYS A 240 MET A 244 0 SHEET 2 E 2 ARG A 247 GLU A 251 -1 O GLU A 251 N LYS A 240 SHEET 1 F 7 VAL A 389 LYS A 390 0 SHEET 2 F 7 LYS A 535 ASP A 540 -1 O ALA A 539 N LYS A 390 SHEET 3 F 7 GLY A 543 THR A 547 -1 O THR A 547 N LYS A 535 SHEET 4 F 7 GLY A 395 PHE A 405 -1 N LEU A 403 O LEU A 544 SHEET 5 F 7 LEU A 577 THR A 590 -1 O GLU A 578 N ASP A 404 SHEET 6 F 7 LYS A 593 ASP A 598 -1 O ILE A 597 N ARG A 585 SHEET 7 F 7 ILE A 603 ARG A 606 -1 O THR A 604 N VAL A 596 SHEET 1 G 2 TYR A 431 VAL A 433 0 SHEET 2 G 2 LYS A 440 CYS A 442 -1 O PHE A 441 N ASP A 432 SHEET 1 H 3 ILE A 662 GLN A 665 0 SHEET 2 H 3 VAL A 698 VAL A 703 -1 O ILE A 699 N GLU A 664 SHEET 3 H 3 ALA A 714 PRO A 716 -1 O ILE A 715 N ILE A 702 SSBOND 1 CYS A 428 CYS A 442 1555 1555 2.05 SSBOND 2 CYS A 506 CYS A 509 1555 1555 2.09 LINK P DA T 1 O1 A5CY T 101 1555 1555 1.60 LINK P DA T 1 O1 B5CY T 101 1555 1555 1.60 LINK O3' DG P 11 P DOC P 12 1555 1555 1.60 CISPEP 1 GLN A 758 LYS A 759 0 3.59 SITE 1 AC1 3 ARG A 406 ARG A 460 LYS A 487 SITE 1 AC2 1 ARG A 32 SITE 1 AC3 2 ARG A 484 DA T 1 SITE 1 AC4 4 LYS A 360 LYS A 363 ARG A 364 LEU A 452 SITE 1 AC5 4 TYR A 388 LYS A 390 GLU A 391 HOH A 934 SITE 1 AC6 4 GLU A 130 GLY A 131 ARG A 335 ARG A 482 SITE 1 AC7 2 ARG A 97 ASP A 113 SITE 1 AC8 5 THR A 136 MET A 137 ASP A 164 GLY A 165 SITE 2 AC8 5 TYR A 320 SITE 1 AC9 3 LYS A 289 TYR A 291 ALA A 292 SITE 1 BC1 3 TYR A 110 PRO A 369 ASN A 370 SITE 1 BC2 5 ARG A 406 SER A 407 LYS A 487 HOH A 980 SITE 2 BC2 5 DA T 2 SITE 1 BC3 4 TYR A 7 GLN A 91 PHE A 116 HOH A1013 SITE 1 BC4 19 ARG A 99 ALA A 102 HIS A 103 PRO A 104 SITE 2 BC4 19 ARG A 266 THR A 267 ILE A 268 VAL A 282 SITE 3 BC4 19 PHE A 283 GLU A 325 PHE A 326 MET A 329 SITE 4 BC4 19 GLU A 330 LEU A 333 THR A 349 HOH A1001 SITE 5 BC4 19 DA T 1 DA T 2 DA T 3 SITE 1 BC5 2 GLY A 245 DG T 4 CRYST1 112.215 142.616 66.702 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 0.008911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014992 0.00000