HEADER TRANSFERASE/DNA 19-APR-13 4K8Z TITLE KOD POLYMERASE IN BINARY COMPLEX WITH DSDNA 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'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)- COMPND 9 3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: POL, POL TK0001, TK0001; 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: PET24A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BERGEN,K.BETZ,W.WELTE,K.DIEDERICHS,A.MARX REVDAT 4 08-NOV-23 4K8Z 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4K8Z 1 REMARK REVDAT 2 09-AUG-17 4K8Z 1 SOURCE REMARK REVDAT 1 26-JUN-13 4K8Z 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. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1243) 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 49743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2516 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 45.0589 - 5.9958 1.00 2842 148 0.1611 0.1696 REMARK 3 2 5.9958 - 4.7607 1.00 2691 151 0.1605 0.1940 REMARK 3 3 4.7607 - 4.1594 1.00 2652 153 0.1390 0.1742 REMARK 3 4 4.1594 - 3.7793 1.00 2671 130 0.1582 0.1792 REMARK 3 5 3.7793 - 3.5086 1.00 2639 144 0.1750 0.2271 REMARK 3 6 3.5086 - 3.3018 1.00 2622 145 0.1865 0.2747 REMARK 3 7 3.3018 - 3.1364 1.00 2616 149 0.1982 0.2506 REMARK 3 8 3.1364 - 2.9999 1.00 2628 127 0.2042 0.2328 REMARK 3 9 2.9999 - 2.8845 1.00 2630 132 0.2030 0.2390 REMARK 3 10 2.8845 - 2.7850 1.00 2575 138 0.2028 0.2529 REMARK 3 11 2.7850 - 2.6979 1.00 2607 150 0.2078 0.2570 REMARK 3 12 2.6979 - 2.6208 1.00 2610 144 0.2095 0.2662 REMARK 3 13 2.6208 - 2.5518 1.00 2619 120 0.2074 0.2623 REMARK 3 14 2.5518 - 2.4895 1.00 2561 149 0.2144 0.2659 REMARK 3 15 2.4895 - 2.4329 1.00 2601 134 0.2203 0.2446 REMARK 3 16 2.4329 - 2.3812 1.00 2607 132 0.2299 0.2692 REMARK 3 17 2.3812 - 2.3335 1.00 2574 135 0.2618 0.3336 REMARK 3 18 2.3335 - 2.2895 0.96 2482 135 0.3126 0.3623 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.89 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 : 0.003 6975 REMARK 3 ANGLE : 0.720 9520 REMARK 3 CHIRALITY : 0.051 1019 REMARK 3 PLANARITY : 0.003 1129 REMARK 3 DIHEDRAL : 15.254 2703 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 1:156) REMARK 3 ORIGIN FOR THE GROUP (A): 182.6034 33.9534 -1.6092 REMARK 3 T TENSOR REMARK 3 T11: 0.3257 T22: 0.2364 REMARK 3 T33: 0.2570 T12: -0.0417 REMARK 3 T13: 0.0351 T23: 0.0442 REMARK 3 L TENSOR REMARK 3 L11: 1.3080 L22: 2.5641 REMARK 3 L33: 2.9648 L12: 0.3547 REMARK 3 L13: -0.3810 L23: 0.9486 REMARK 3 S TENSOR REMARK 3 S11: -0.2071 S12: 0.2456 S13: -0.0508 REMARK 3 S21: -0.5490 S22: 0.1192 S23: -0.3131 REMARK 3 S31: -0.0962 S32: -0.0129 S33: 0.0885 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 157:304) REMARK 3 ORIGIN FOR THE GROUP (A): 171.6163 49.5671 23.9651 REMARK 3 T TENSOR REMARK 3 T11: 0.2481 T22: 0.2263 REMARK 3 T33: 0.1672 T12: 0.0374 REMARK 3 T13: -0.0484 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 2.8674 L22: 4.0069 REMARK 3 L33: 2.8658 L12: -0.7566 REMARK 3 L13: -1.1851 L23: 1.0618 REMARK 3 S TENSOR REMARK 3 S11: 0.0876 S12: 0.0648 S13: 0.0434 REMARK 3 S21: -0.2638 S22: -0.1324 S23: 0.1097 REMARK 3 S31: -0.2929 S32: -0.2614 S33: 0.0444 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 305:532) REMARK 3 ORIGIN FOR THE GROUP (A): 170.9268 15.4571 15.2712 REMARK 3 T TENSOR REMARK 3 T11: 0.2807 T22: 0.2540 REMARK 3 T33: 0.2775 T12: 0.0243 REMARK 3 T13: 0.0535 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.5468 L22: 1.4185 REMARK 3 L33: -0.0170 L12: 0.2261 REMARK 3 L13: 0.1166 L23: -0.3985 REMARK 3 S TENSOR REMARK 3 S11: -0.0066 S12: -0.0316 S13: -0.1320 REMARK 3 S21: 0.0139 S22: 0.0045 S23: -0.1053 REMARK 3 S31: 0.1046 S32: -0.0321 S33: -0.0062 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 533:756) REMARK 3 ORIGIN FOR THE GROUP (A): 148.7619 22.1699 31.8260 REMARK 3 T TENSOR REMARK 3 T11: 0.2376 T22: 0.3653 REMARK 3 T33: 0.3480 T12: -0.0084 REMARK 3 T13: 0.0011 T23: -0.0685 REMARK 3 L TENSOR REMARK 3 L11: 1.3779 L22: 3.7472 REMARK 3 L33: 1.0882 L12: -0.8886 REMARK 3 L13: -0.0358 L23: -0.1827 REMARK 3 S TENSOR REMARK 3 S11: -0.1147 S12: -0.3371 S13: 0.1320 REMARK 3 S21: 0.3424 S22: 0.1003 S23: 0.2017 REMARK 3 S31: -0.1712 S32: -0.0749 S33: 0.0070 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESSEQ 3:16) REMARK 3 ORIGIN FOR THE GROUP (A): 145.2691 22.9034 15.0004 REMARK 3 T TENSOR REMARK 3 T11: 0.3534 T22: 0.2729 REMARK 3 T33: 0.5137 T12: -0.0414 REMARK 3 T13: -0.0421 T23: -0.0736 REMARK 3 L TENSOR REMARK 3 L11: 7.9458 L22: 2.9274 REMARK 3 L33: 2.8478 L12: -3.2151 REMARK 3 L13: -0.4750 L23: 0.9186 REMARK 3 S TENSOR REMARK 3 S11: -0.2184 S12: 0.3380 S13: -0.2042 REMARK 3 S21: -0.4786 S22: 0.0206 S23: 0.5609 REMARK 3 S31: -0.1466 S32: -0.3984 S33: 0.1475 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESSEQ 1:11) REMARK 3 ORIGIN FOR THE GROUP (A): 141.2384 22.9285 16.3368 REMARK 3 T TENSOR REMARK 3 T11: 0.3786 T22: 0.3511 REMARK 3 T33: 0.6634 T12: 0.0552 REMARK 3 T13: -0.0703 T23: -0.1003 REMARK 3 L TENSOR REMARK 3 L11: 7.3534 L22: 1.1833 REMARK 3 L33: 3.7205 L12: -0.1354 REMARK 3 L13: -1.6465 L23: -0.7364 REMARK 3 S TENSOR REMARK 3 S11: -0.0626 S12: 0.9853 S13: -0.8696 REMARK 3 S21: -0.4591 S22: 0.2038 S23: 0.5836 REMARK 3 S31: -0.1128 S32: -0.3518 S33: -0.1720 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 4K8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 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) : 1.00002 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR DYNAMICALLY REMARK 200 BENDABLE MIRROR 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, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 49.324 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.810 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 16.15 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : 0.13100 REMARK 200 FOR THE DATA SET : 16.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 13.16 REMARK 200 R MERGE FOR SHELL (I) : 1.88800 REMARK 200 R SYM FOR SHELL (I) : 1.96500 REMARK 200 FOR SHELL : 1.810 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: 1WNS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM NA-CACODYLATE, 20MM MGCL2, 1MM REMARK 280 COBALT(III)-HEXAMMINECHLORIDE, 1MM SPERMINE, 20%V/V 2-PROPANOL, , REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING 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 72.43500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 72.43500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.89000 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: 5910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 TYR A 757 REMARK 465 GLN A 758 REMARK 465 LYS A 759 REMARK 465 THR A 760 REMARK 465 ARG A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 SER A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 PRO A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 THR A 774 REMARK 465 DA T 1 REMARK 465 DA T 2 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 DC P 10 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DG P 11 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 2DA P 12 O3' - P - OP2 ANGL. DEV. = 14.5 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 ARG A 58 -83.82 -81.32 REMARK 500 ASP A 164 -156.00 -148.68 REMARK 500 PHE A 214 -71.34 -138.70 REMARK 500 GLU A 303 -85.92 -86.07 REMARK 500 ASN A 399 72.13 54.79 REMARK 500 GLN A 436 -57.27 64.19 REMARK 500 TRP A 504 33.41 -96.81 REMARK 500 THR A 541 -69.58 67.43 REMARK 500 LYS A 592 -5.86 71.98 REMARK 500 ARG A 689 -147.93 -93.86 REMARK 500 GLN A 736 -70.44 -114.98 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 T 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC T 8 OP2 REMARK 620 2 DC T 8 O5' 61.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG T 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WNS RELATED DB: PDB REMARK 900 RELATED ID: 1QHT RELATED DB: PDB REMARK 900 RELATED ID: 4K8X RELATED DB: PDB DBREF 4K8Z A 1 406 UNP P77933 DPOL_PYRKO 1 406 DBREF 4K8Z A 407 491 UNP P77933 DPOL_PYRKO 767 851 DBREF 4K8Z A 492 774 UNP P77933 DPOL_PYRKO 1389 1671 DBREF 4K8Z T 1 16 PDB 4K8Z 4K8Z 1 16 DBREF 4K8Z P 1 12 PDB 4K8Z 4K8Z 1 12 SEQADV 4K8Z ALA A 141 UNP P77933 ASP 141 ENGINEERED MUTATION SEQADV 4K8Z ALA A 143 UNP P77933 GLU 143 ENGINEERED MUTATION SEQRES 1 A 774 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 774 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 774 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 774 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU GLU VAL LYS SEQRES 5 A 774 LYS ILE THR ALA GLU ARG HIS GLY THR VAL VAL THR VAL SEQRES 6 A 774 LYS ARG VAL GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 774 PRO VAL GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 774 ASP VAL PRO ALA ILE ARG ASP LYS ILE ARG GLU HIS PRO SEQRES 9 A 774 ALA VAL ILE ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 774 LYS ARG TYR LEU ILE ASP LYS GLY LEU VAL PRO MET GLU SEQRES 11 A 774 GLY ASP GLU GLU LEU LYS MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 774 THR LEU TYR HIS GLU GLY GLU GLU PHE ALA GLU GLY PRO SEQRES 13 A 774 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 774 VAL ILE THR TRP LYS ASN VAL ASP LEU PRO TYR VAL ASP SEQRES 15 A 774 VAL VAL SER THR GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 774 ARG VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 774 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 774 ARG CYS GLU LYS LEU GLY ILE ASN PHE ALA LEU GLY ARG SEQRES 19 A 774 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 774 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 774 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 774 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY GLN PRO SEQRES 23 A 774 LYS GLU LYS VAL TYR ALA GLU GLU ILE THR THR ALA TRP SEQRES 24 A 774 GLU THR GLY GLU ASN LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 774 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 774 PHE LEU PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 774 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 774 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 774 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU LYS GLU LEU SEQRES 30 A 774 ALA ARG ARG ARG GLN SER TYR GLU GLY GLY TYR VAL LYS SEQRES 31 A 774 GLU PRO GLU ARG GLY LEU TRP GLU ASN ILE VAL TYR LEU SEQRES 32 A 774 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 774 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS LYS SEQRES 34 A 774 GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS ARG PHE CYS SEQRES 35 A 774 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 774 LEU LEU GLU GLU ARG GLN LYS ILE LYS LYS LYS MET LYS SEQRES 37 A 774 ALA THR ILE ASP PRO ILE GLU ARG LYS LEU LEU ASP TYR SEQRES 38 A 774 ARG GLN ARG ALA ILE LYS ILE LEU ALA ASN SER TYR TYR SEQRES 39 A 774 GLY TYR TYR GLY TYR ALA ARG ALA ARG TRP TYR CYS LYS SEQRES 40 A 774 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 774 ILE THR MET THR ILE LYS GLU ILE GLU GLU LYS TYR GLY SEQRES 42 A 774 PHE LYS VAL ILE TYR SER ASP THR ASP GLY PHE PHE ALA SEQRES 43 A 774 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 774 ALA MET GLU PHE LEU LYS TYR ILE ASN ALA LYS LEU PRO SEQRES 45 A 774 GLY ALA LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS ARG SEQRES 46 A 774 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 774 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 774 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 774 ARG VAL LEU GLU ALA LEU LEU LYS ASP GLY ASP VAL GLU SEQRES 50 A 774 LYS ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 774 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 774 GLU GLN ILE THR ARG ASP LEU LYS ASP TYR LYS ALA THR SEQRES 53 A 774 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 774 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 774 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 774 PRO PHE ASP GLU PHE ASP PRO THR LYS HIS LYS TYR ASP SEQRES 57 A 774 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 774 GLU ARG ILE LEU ARG ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 774 LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU SER ALA SEQRES 60 A 774 TRP LEU LYS PRO LYS GLY THR SEQRES 1 T 16 DA DA DA DT DT 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 2DA MODRES 4K8Z 2DA P 12 DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HET 2DA P 12 20 HET NCO A 801 7 HET EDO A 802 4 HET EDO A 803 4 HET MG T 101 1 HETNAM 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM NCO COBALT HEXAMMINE(III) HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 2DA C10 H14 N5 O5 P FORMUL 4 NCO CO H18 N6 3+ FORMUL 5 EDO 2(C2 H6 O2) FORMUL 7 MG MG 2+ FORMUL 8 HOH *367(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 GLU A 102 1 12 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 GLY A 227 1 14 HELIX 7 7 LEU A 260 ILE A 268 1 9 HELIX 8 8 THR A 274 PHE A 283 1 10 HELIX 9 9 TYR A 291 GLY A 302 1 12 HELIX 10 10 ASN 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 380 1 8 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 GLY A 533 1 28 HELIX 19 19 ASP A 552 LEU A 571 1 20 HELIX 20 20 LEU A 608 ARG A 612 5 5 HELIX 21 21 SER A 616 LYS A 632 1 17 HELIX 22 22 ASP A 635 LYS A 652 1 18 HELIX 23 23 PRO A 656 VAL A 661 5 6 HELIX 24 24 ASP A 669 TYR A 673 5 5 HELIX 25 25 GLY A 677 ARG A 689 1 13 HELIX 26 26 ARG A 709 ASP A 712 5 4 HELIX 27 27 ASP A 718 PHE A 720 5 3 HELIX 28 28 ASP A 728 ASN A 735 1 8 HELIX 29 29 GLN A 736 ARG A 746 1 11 HELIX 30 30 ALA A 747 GLY A 749 5 3 HELIX 31 31 ARG A 751 LEU A 755 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 ARG A 17 N ASP A 6 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 LYS A 84 N GLU A 69 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 ALA A 56 GLU A 57 0 SHEET 2 C 2 VAL A 62 VAL A 63 -1 O VAL A 63 N ALA A 56 SHEET 1 D 6 VAL A 181 VAL A 183 0 SHEET 2 D 6 GLY A 167 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 D 6 ILE A 157 ASP A 164 -1 N ILE A 160 O ILE A 171 SHEET 4 D 6 MET A 137 THR A 144 -1 N ALA A 141 O SER A 161 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 PHE A 258 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 ALA A 249 N GLN A 242 SHEET 1 F 6 LYS A 535 SER A 539 0 SHEET 2 F 6 GLY A 543 THR A 547 -1 O THR A 547 N LYS A 535 SHEET 3 F 6 GLY A 395 PHE A 405 -1 N VAL A 401 O ALA A 546 SHEET 4 F 6 LEU A 577 THR A 590 -1 O TYR A 583 N ILE A 400 SHEET 5 F 6 LYS A 593 ILE A 597 -1 O ALA A 595 N PHE A 587 SHEET 6 F 6 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 ARG 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 2.04 LINK O3' DG P 11 P 2DA P 12 1555 1555 1.61 LINK OP2 DC T 8 MG MG T 101 1555 1555 2.20 LINK O5' DC T 8 MG MG T 101 1555 1555 2.64 SITE 1 AC1 5 ASN A 568 LEU A 571 GLY A 573 LEU A 575 SITE 2 AC1 5 GLU A 576 SITE 1 AC2 4 GLY A 167 ALA A 168 TYR A 180 LYS A 317 SITE 1 AC3 2 ASN A 210 HOH A1005 SITE 1 AC4 2 DG T 7 DC T 8 CRYST1 144.870 111.780 67.100 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 0.006903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008946 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014903 0.00000