HEADER DNA REPLICATION 26-JUN-08 2VWK TITLE URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY TITLE 2 CRYSTALLOGRAPHY. V93Q POLYMERASE VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TGO POLYMERASE DNA COMPLEX, TO POL; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS GORGONARIUS; SOURCE 3 ORGANISM_TAXID: 71997; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET 17B KEYWDS DNA REPLICATION, MULTIFUNCTIONAL ENZYME, NUCLEOTIDYLTRANSFERASE, DNA- KEYWDS 2 DIRECTED DNA POLYMERASE, TRANSFERASE, EXONUCLEASE, DNA-BINDING, DNA KEYWDS 3 POLYMERASE, URACIL, ARCHAEA, NUCLEASE, HYDROLASE, DNA REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR S.J.FIRBANK,J.WARDLE,P.HESLOP,R.J.LEWIS,B.A.CONNOLLY REVDAT 4 13-DEC-23 2VWK 1 REMARK REVDAT 3 24-FEB-09 2VWK 1 VERSN REVDAT 2 12-AUG-08 2VWK 1 JRNL REVDAT 1 22-JUL-08 2VWK 0 JRNL AUTH S.J.FIRBANK,J.WARDLE,P.HESLOP,R.J.LEWIS,B.A.CONNOLLY JRNL TITL URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY JRNL TITL 2 X-RAY CRYSTALLOGRAPHY. JRNL REF J.MOL.BIOL. V. 381 529 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18614176 JRNL DOI 10.1016/J.JMB.2008.06.004 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28433 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 + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1520 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2110 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6083 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.738 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.340 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.248 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.314 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.870 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6254 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8487 ; 1.118 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 772 ; 5.731 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 277 ;32.145 ;23.646 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1043 ;17.150 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;17.487 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 928 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4735 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2637 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4316 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 225 ; 0.145 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 84 ; 0.182 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.180 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3851 ; 0.487 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6195 ; 0.934 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2492 ; 1.243 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2292 ; 2.115 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VWK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1290036701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : DIAMOND AND GE(220) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29945 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 62.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1TGO REMARK 200 REMARK 200 REMARK: ESSENTIALLY ISOMORPHOUS WITH 1TGO, THEREFORE 1TGO USED AS REMARK 200 STARTING MODEL FOR RIGID BODY REFINEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9M AMMONIUM SULPHATE, 100MM BIS REMARK 280 -TRIS, PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.21600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.20400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.37350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.20400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.21600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.37350 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN X, VAL 93 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN X, ASP 215 TO ALA 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 21 CG CD CE NZ REMARK 470 LYS A 53 CE NZ REMARK 470 ARG A 64 NE CZ NH1 NH2 REMARK 470 ARG A 78 NE CZ NH1 NH2 REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 GLU A 134 CD OE1 OE2 REMARK 470 LYS A 136 CD CE NZ REMARK 470 LEU A 145 CG CD1 CD2 REMARK 470 GLU A 148 CG CD OE1 OE2 REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 GLU A 154 CD OE1 OE2 REMARK 470 GLU A 166 CD OE1 OE2 REMARK 470 LYS A 196 CE NZ REMARK 470 LYS A 199 CE NZ REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 LYS A 221 CE NZ REMARK 470 LYS A 225 CE NZ REMARK 470 LYS A 229 CD CE NZ REMARK 470 LYS A 240 CD CE NZ REMARK 470 GLN A 242 CD OE1 NE2 REMARK 470 ARG A 243 CG CD NE CZ NH1 NH2 REMARK 470 MET A 244 CG SD CE REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 ARG A 266 NE CZ NH1 NH2 REMARK 470 ILE A 268 CG1 CG2 CD1 REMARK 470 ASN A 269 CG OD1 ND2 REMARK 470 THR A 272 CB OG1 CG2 REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 GLN A 285 CG CD OE1 NE2 REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 TYR A 291 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TRP A 299 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 REMARK 470 TRP A 299 CH2 REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 ARG A 307 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 310 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 317 CD CE NZ REMARK 470 LYS A 324 CD CE NZ REMARK 470 GLU A 374 CG CD OE1 OE2 REMARK 470 ARG A 375 NE CZ NH1 NH2 REMARK 470 ARG A 379 CZ NH1 NH2 REMARK 470 GLU A 382 CD OE1 OE2 REMARK 470 ARG A 425 CD NE CZ NH1 NH2 REMARK 470 GLN A 461 CD OE1 NE2 REMARK 470 LYS A 462 CE NZ REMARK 470 GLU A 475 CG CD OE1 OE2 REMARK 470 LYS A 477 CE NZ REMARK 470 ARG A 484 CD NE CZ NH1 NH2 REMARK 470 LYS A 501 CD CE NZ REMARK 470 ARG A 526 NE CZ NH1 NH2 REMARK 470 LYS A 531 CD CE NZ REMARK 470 LYS A 535 NZ REMARK 470 ARG A 613 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 621 CD OE1 OE2 REMARK 470 LYS A 652 CE NZ REMARK 470 GLU A 658 CG CD OE1 OE2 REMARK 470 GLN A 665 CG CD OE1 NE2 REMARK 470 LYS A 671 CD CE NZ REMARK 470 LYS A 674 CG CD CE NZ REMARK 470 LYS A 692 CD CE NZ REMARK 470 LYS A 724 CG CD CE NZ REMARK 470 LYS A 726 CD CE NZ REMARK 470 ARG A 746 CD NE CZ NH1 NH2 REMARK 470 LYS A 752 CD CE NZ REMARK 470 GLU A 753 CG CD OE1 OE2 REMARK 470 GLN A 758 CG CD OE1 NE2 REMARK 470 LYS A 759 CG CD CE NZ REMARK 470 ARG A 761 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 770 CG CD CE NZ REMARK 470 LYS A 772 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 GLU A 133 120.95 -9.06 REMARK 500 PHE A 214 -84.12 -115.83 REMARK 500 ARG A 247 -153.72 -92.92 REMARK 500 THR A 267 -86.90 -85.10 REMARK 500 PRO A 271 -85.66 -70.91 REMARK 500 TYR A 273 59.53 -97.49 REMARK 500 PHE A 283 -30.84 -136.10 REMARK 500 GLU A 288 61.62 66.95 REMARK 500 GLU A 382 45.12 -83.17 REMARK 500 ASN A 424 57.32 29.74 REMARK 500 GLN A 436 -66.29 66.74 REMARK 500 TRP A 504 34.72 -86.65 REMARK 500 CYS A 506 92.17 -164.66 REMARK 500 LYS A 591 112.86 -38.19 REMARK 500 LYS A 724 -6.50 83.69 REMARK 500 GLN A 736 -65.88 -101.85 REMARK 500 THR A 760 54.59 -151.26 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 NA A1774 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1775 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1776 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1777 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1778 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1779 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1780 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1781 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WN7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ARCHAEAL FAMILY B DNA POLYMERASE MUTANT REMARK 900 RELATED ID: 1TGO RELATED DB: PDB REMARK 900 THERMOSTABLE B TYPE DEOXYRIBONUCLEIC ACID POLYMERASE FROM REMARK 900 THERMOCOCCUS GORGONARIUS REMARK 900 RELATED ID: 2VWJ RELATED DB: PDB REMARK 900 URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY REMARK 900 CRYSTALLOGRAPHY. REMARK 999 REMARK 999 SEQUENCE REMARK 999 V93 MUTATED TO GLUTAMINE - A MUTATION WHICH PREVENTS THE REMARK 999 RECOGNITION OF URACIL BY THE POLYMERASE. MUTATION OF D215 REMARK 999 TO ALANINE TO REMOVE EXONUCLEASE ACTIVITY. DBREF 2VWK A 1 773 UNP P56689 DPOL_THEGO 1 773 SEQADV 2VWK GLN A 93 UNP P56689 VAL 93 ENGINEERED MUTATION SEQADV 2VWK LYS A 151 UNP P56689 GLU 151 CONFLICT SEQADV 2VWK ARG A 174 UNP P56689 LYS 174 CONFLICT SEQADV 2VWK ALA A 215 UNP P56689 ASP 215 ENGINEERED MUTATION SEQRES 1 A 773 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 773 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 773 LYS ILE ASP TYR ASP ARG ASN PHE GLU PRO TYR ILE TYR SEQRES 4 A 773 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU ASP VAL LYS SEQRES 5 A 773 LYS ILE THR ALA GLU ARG HIS GLY THR THR VAL ARG VAL SEQRES 6 A 773 VAL ARG ALA GLU LYS VAL LYS LYS LYS PHE LEU GLY ARG SEQRES 7 A 773 PRO ILE GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 773 ASP GLN PRO ALA ILE ARG ASP LYS ILE LYS GLU HIS PRO SEQRES 9 A 773 ALA VAL VAL ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 773 LYS ARG TYR LEU ILE ASP LYS GLY LEU ILE PRO MET GLU SEQRES 11 A 773 GLY ASP GLU GLU LEU LYS MET LEU ALA PHE ASP ILE GLU SEQRES 12 A 773 THR LEU TYR HIS GLU GLY GLU LYS PHE ALA GLU GLY PRO SEQRES 13 A 773 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 773 VAL ILE THR TRP ARG ASN ILE ASP LEU PRO TYR VAL ASP SEQRES 15 A 773 VAL VAL SER THR GLU LYS GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 773 LYS VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 773 TYR ASN GLY ASP ASN PHE ALA PHE ALA TYR LEU LYS LYS SEQRES 18 A 773 ARG SER GLU LYS LEU GLY VAL LYS PHE ILE LEU GLY ARG SEQRES 19 A 773 GLU GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 773 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 773 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 773 THR LEU GLU ALA VAL TYR GLU ALA ILE PHE GLY GLN PRO SEQRES 23 A 773 LYS GLU LYS VAL TYR ALA GLU GLU ILE ALA GLN ALA TRP SEQRES 24 A 773 GLU THR GLY GLU GLY LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 773 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 773 PHE PHE PRO MET GLU ALA GLN LEU SER ARG LEU VAL GLY SEQRES 27 A 773 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 773 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 773 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU ARG GLU LEU SEQRES 30 A 773 ALA ARG ARG ARG GLU SER TYR ALA GLY GLY TYR VAL LYS SEQRES 31 A 773 GLU PRO GLU ARG GLY LEU TRP GLU ASN ILE VAL TYR LEU SEQRES 32 A 773 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 773 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS GLU SEQRES 34 A 773 GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS LYS PHE CYS SEQRES 35 A 773 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 773 LEU LEU GLU GLU ARG GLN LYS VAL LYS LYS LYS MET LYS SEQRES 37 A 773 ALA THR ILE ASP PRO ILE GLU LYS LYS LEU LEU ASP TYR SEQRES 38 A 773 ARG GLN ARG ALA ILE LYS ILE LEU ALA ASN SER PHE TYR SEQRES 39 A 773 GLY TYR TYR GLY TYR ALA LYS ALA ARG TRP TYR CYS LYS SEQRES 40 A 773 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLN TYR SEQRES 41 A 773 ILE GLU THR THR ILE ARG GLU ILE GLU GLU LYS PHE GLY SEQRES 42 A 773 PHE LYS VAL LEU TYR ALA ASP THR ASP GLY PHE PHE ALA SEQRES 43 A 773 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 773 ALA LYS GLU PHE LEU ASP TYR ILE ASN ALA LYS LEU PRO SEQRES 45 A 773 GLY LEU LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS ARG SEQRES 46 A 773 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 773 GLU GLU ASP LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 773 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 773 ARG VAL LEU GLU ALA ILE LEU LYS HIS GLY ASP VAL GLU SEQRES 50 A 773 GLU ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 773 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE TYR SEQRES 52 A 773 GLU GLN ILE THR ARG ASP LEU LYS ASP TYR LYS ALA THR SEQRES 53 A 773 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 773 GLY ILE LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 773 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 773 PRO PHE ASP GLU PHE ASP PRO ALA LYS HIS LYS TYR ASP SEQRES 57 A 773 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 773 GLU ARG ILE LEU ARG ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 773 LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU GLY ALA SEQRES 60 A 773 TRP LEU LYS PRO LYS THR HET NA A1774 1 HET SO4 A1775 5 HET SO4 A1776 5 HET SO4 A1777 5 HET SO4 A1778 5 HET SO4 A1779 5 HET SO4 A1780 5 HET SO4 A1781 5 HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION FORMUL 2 NA NA 1+ FORMUL 3 SO4 7(O4 S 2-) FORMUL 10 HOH *57(H2 O) HELIX 1 1 ASP A 44 SER A 46 5 3 HELIX 2 2 ALA A 47 LYS A 52 1 6 HELIX 3 3 GLN A 91 GLU A 102 1 12 HELIX 4 4 PRO A 115 GLY A 125 1 11 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 ILE A 282 1 9 HELIX 9 9 TYR A 291 THR A 301 1 11 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 GLU A 382 1 10 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 ALA A 569 1 18 HELIX 20 20 SER A 616 LYS A 632 1 17 HELIX 21 21 ASP A 635 LYS A 652 1 18 HELIX 22 22 PRO A 656 VAL A 661 5 6 HELIX 23 23 ASP A 669 TYR A 673 5 5 HELIX 24 24 PRO A 678 ALA A 688 1 11 HELIX 25 25 ASP A 718 PHE A 720 5 3 HELIX 26 26 ASP A 728 ASN A 735 1 8 HELIX 27 27 GLN A 736 ALA A 747 1 12 HELIX 28 28 ARG A 751 ARG A 756 5 6 HELIX 29 29 LEU A 765 LYS A 770 1 6 SHEET 1 AA 3 ILE A 2 GLU A 10 0 SHEET 2 AA 3 LYS A 13 GLU A 22 -1 O LYS A 13 N GLU A 10 SHEET 3 AA 3 GLU A 25 ASP A 31 -1 O GLU A 25 N GLU A 22 SHEET 1 AB 4 ARG A 67 PHE A 75 0 SHEET 2 AB 4 ARG A 78 TYR A 86 -1 O ARG A 78 N PHE A 75 SHEET 3 AB 4 TYR A 37 LEU A 42 -1 O ILE A 38 N LEU A 85 SHEET 4 AB 4 VAL A 106 TYR A 110 -1 N VAL A 107 O LEU A 41 SHEET 1 AC 2 THR A 55 ARG A 58 0 SHEET 2 AC 2 THR A 61 ARG A 64 -1 O THR A 61 N ARG A 58 SHEET 1 AD 6 VAL A 181 VAL A 183 0 SHEET 2 AD 6 ALA A 168 THR A 172 1 O VAL A 170 N ASP A 182 SHEET 3 AD 6 ILE A 157 ALA A 163 -1 O ILE A 160 N ILE A 171 SHEET 4 AD 6 MET A 137 THR A 144 -1 O ALA A 139 N ALA A 163 SHEET 5 AD 6 VAL A 205 THR A 208 1 O VAL A 205 N LEU A 138 SHEET 6 AD 6 ILE A 256 ASP A 259 1 O ILE A 256 N LEU A 206 SHEET 1 AE 2 LYS A 240 MET A 244 0 SHEET 2 AE 2 ARG A 247 GLU A 251 -1 O ARG A 247 N MET A 244 SHEET 1 AF 6 LYS A 535 ASP A 540 0 SHEET 2 AF 6 GLY A 543 THR A 547 -1 O GLY A 543 N ASP A 540 SHEET 3 AF 6 LEU A 396 PHE A 405 -1 O VAL A 401 N ALA A 546 SHEET 4 AF 6 LEU A 577 THR A 590 -1 O GLU A 578 N ASP A 404 SHEET 5 AF 6 LYS A 593 ILE A 597 -1 O LYS A 593 N VAL A 589 SHEET 6 AF 6 ILE A 603 ARG A 606 -1 O THR A 604 N VAL A 596 SHEET 1 AG 2 TYR A 431 VAL A 433 0 SHEET 2 AG 2 LYS A 440 CYS A 442 -1 O PHE A 441 N ASP A 432 SHEET 1 AH 3 ILE A 662 GLN A 665 0 SHEET 2 AH 3 VAL A 698 VAL A 703 -1 O ILE A 699 N GLU A 664 SHEET 3 AH 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 2.08 SSBOND 2 CYS A 506 CYS A 509 1555 1555 2.11 LINK NA NA A1774 O2 SO4 A1776 1555 1555 2.24 SITE 1 AC1 3 ARG A 460 LYS A 487 SO4 A1776 SITE 1 AC2 2 ARG A 606 GLY A 607 SITE 1 AC3 4 SER A 407 LYS A 487 ASN A 491 NA A1774 SITE 1 AC4 4 TYR A 7 PRO A 115 PHE A 116 HOH A2055 SITE 1 AC5 5 PRO A 435 GLN A 436 GLU A 628 LYS A 632 SITE 2 AC5 5 HIS A 633 SITE 1 AC6 3 SER A 348 TYR A 499 HOH A2056 SITE 1 AC7 4 GLY A 386 GLN A 436 LYS A 584 ARG A 585 SITE 1 AC8 6 GLY A 387 TYR A 388 THR A 541 LYS A 591 SITE 2 AC8 6 LYS A 592 HOH A2057 CRYST1 58.432 104.747 154.408 90.00 90.00 90.00 P 21 21 21 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 0.017114 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006476 0.00000