HEADER TRANSFERASE/DNA 14-JUN-10 2XHB TITLE CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN TITLE 2 COMPLEX WITH HYPOXANTHINE-CONTAINING DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TO POL; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HYPOXANTHINE-CONTAINING DNA; COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'; COMPND 14 CHAIN: E; COMPND 15 ENGINEERED: 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_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET17B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS TRANSFERASE-DNA COMPLEX, REPLICATION, EXONUCLEASE, DNA DAMAGE, EXO KEYWDS 2 MINUS EXPDTA X-RAY DIFFRACTION AUTHOR T.KILLELEA,S.GHOSH,S.S.TAN,P.HESLOP,S.J.FIRBANK,E.T.KOOL,B.A.CONNOLLY REVDAT 3 13-NOV-24 2XHB 1 REMARK REVDAT 2 20-DEC-23 2XHB 1 REMARK LINK REVDAT 1 21-JUL-10 2XHB 0 JRNL AUTH T.KILLELEA,S.GHOSH,S.S.TAN,P.HESLOP,S.J.FIRBANK,E.T.KOOL, JRNL AUTH 2 B.A.CONNOLLY JRNL TITL PROBING THE INTERACTION OF ARCHAEAL DNA POLYMERASES WITH JRNL TITL 2 DEAMINATED BASES USING X-RAY CRYSTALLOGRAPHY AND JRNL TITL 3 NON-HYDROGEN BONDING ISOSTERIC BASE ANALOGUES. JRNL REF BIOCHEMISTRY V. 49 5772 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20527806 JRNL DOI 10.1021/BI100421R REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 22478 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1229 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) : 2.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1657 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5949 REMARK 3 NUCLEIC ACID ATOMS : 513 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -1.20000 REMARK 3 B33 (A**2) : 1.75000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.967 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.447 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.287 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.888 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.827 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6656 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4468 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9111 ; 0.959 ; 2.068 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10859 ; 0.783 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 5.075 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;30.413 ;23.427 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1050 ;14.708 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;14.395 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1006 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6956 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1335 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3692 ; 0.428 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1492 ; 0.050 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5966 ; 0.801 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2974 ; 0.892 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3157 ; 1.550 ; 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 : 1.40 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. RESIDUES 146-150 AND 374-384 WERE NOT MODELLED OWING REMARK 3 TO DISORDER. REMARK 4 REMARK 4 2XHB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1290044235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23740 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2VWJ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE PH 9.0, 20% PEG6000 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 39.72500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.31500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.18500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.31500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.18500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 A, ASP 215 TO ALA 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 146 REMARK 465 HIS A 147 REMARK 465 GLU A 148 REMARK 465 GLY A 149 REMARK 465 GLU A 150 REMARK 465 GLU A 374 REMARK 465 ARG A 375 REMARK 465 GLU A 376 REMARK 465 LEU A 377 REMARK 465 ALA A 378 REMARK 465 ARG A 379 REMARK 465 ARG A 380 REMARK 465 ARG A 381 REMARK 465 GLU A 382 REMARK 465 SER A 383 REMARK 465 TYR A 384 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 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 PRO A 771 REMARK 465 LYS A 772 REMARK 465 THR A 773 REMARK 465 DA D 0 REMARK 465 DA D 1 REMARK 465 DT D 14 REMARK 465 DT D 15 REMARK 465 DT D 16 REMARK 465 DT D 17 REMARK 465 DG D 18 REMARK 465 DC D 19 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 72 CD CE NZ REMARK 470 LYS A 99 CE NZ REMARK 470 LYS A 124 CE NZ REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 LYS A 199 CG CD CE NZ REMARK 470 LYS A 221 CD CE NZ REMARK 470 LYS A 225 CD CE NZ REMARK 470 LYS A 229 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 GLU A 293 CG CD OE1 OE2 REMARK 470 GLU A 300 CD OE1 OE2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 GLU A 306 CG CD OE1 OE2 REMARK 470 ARG A 310 NE CZ NH1 NH2 REMARK 470 LYS A 317 CE NZ REMARK 470 LYS A 360 NZ REMARK 470 GLN A 436 CG CD OE1 NE2 REMARK 470 LYS A 440 CD CE NZ REMARK 470 GLU A 458 CG CD OE1 OE2 REMARK 470 GLU A 459 CD OE1 OE2 REMARK 470 LYS A 462 CD CE NZ REMARK 470 LYS A 465 CG CD CE NZ REMARK 470 LYS A 466 CD CE NZ REMARK 470 LYS A 468 CG CD CE NZ REMARK 470 LYS A 476 CD CE NZ REMARK 470 LYS A 477 CD CE NZ REMARK 470 LYS A 487 CE NZ REMARK 470 LYS A 501 CD CE NZ REMARK 470 LYS A 570 CE NZ REMARK 470 LYS A 584 NZ REMARK 470 LYS A 591 CE NZ REMARK 470 LYS A 592 NZ REMARK 470 LYS A 602 CG CD CE NZ REMARK 470 LYS A 632 NZ REMARK 470 LYS A 644 CE NZ REMARK 470 LYS A 671 CG CD CE NZ REMARK 470 LYS A 674 CD CE NZ REMARK 470 LYS A 724 CD CE NZ REMARK 470 LYS A 726 CE NZ REMARK 470 ARG A 746 NE CZ NH1 NH2 REMARK 470 GLU A 753 CG CD OE1 OE2 REMARK 470 DA E 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 1 C2 N3 C4 REMARK 470 DA E 2 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 2 C2 N3 C4 REMARK 470 DA E 3 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 3 C2 N3 C4 REMARK 470 DA E 4 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 4 C2 N3 C4 REMARK 470 DA E 5 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 5 C2 N3 C4 REMARK 470 DA E 6 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 6 C2 N3 C4 REMARK 470 DA E 7 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 7 C2 N3 C4 REMARK 470 DA E 8 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 8 C2 N3 C4 REMARK 470 DA E 9 C8 N7 C5 C6 N6 N1 C2 REMARK 470 DA E 9 N3 C4 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DI D 2 P DI D 2 OP3 -0.129 REMARK 500 REMARK 500 REMARK: NULL 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 DI D 2 O5' - P - OP1 ANGL. DEV. = 10.2 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA D 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA D 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC D 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG D 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC D 20 O4' - C1' - N1 ANGL. DEV. = 2.3 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 ASP A 164 -156.14 -156.25 REMARK 500 PHE A 214 -73.97 -160.14 REMARK 500 TYR A 273 44.63 -100.32 REMARK 500 ASN A 399 72.97 50.27 REMARK 500 ASN A 424 51.66 35.74 REMARK 500 GLN A 436 -68.20 67.58 REMARK 500 TRP A 504 50.24 -96.62 REMARK 500 CYS A 506 94.53 -165.13 REMARK 500 GLN A 736 -65.93 -122.44 REMARK 500 ALA A 747 1.47 -68.57 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 NA A1758 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 101 O REMARK 620 2 HIS A 103 O 84.5 REMARK 620 3 VAL A 106 O 93.2 93.3 REMARK 620 4 HOH A2005 O 83.5 161.3 101.6 REMARK 620 5 HOH A2006 O 84.2 92.7 173.2 71.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1758 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: 2VWK RELATED DB: PDB REMARK 900 URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY REMARK 900 CRYSTALLOGRAPHY. V93Q POLYMERASE VARIANT REMARK 900 RELATED ID: 2VWJ RELATED DB: PDB REMARK 900 URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY REMARK 900 CRYSTALLOGRAPHY. REMARK 900 RELATED ID: 1TGO RELATED DB: PDB REMARK 900 THERMOSTABLE B TYPE DEOXYRIBONUCLEIC ACID POLYMERASE FROM REMARK 900 THERMOCOCCUS GORGONARIUS REMARK 999 REMARK 999 SEQUENCE REMARK 999 EXO MINUS MUTANT D215A REMARK 999 CHAIN E: IT WAS NOT POSSIBLE TO POSITION THIS DNA IN THE OBSERVED REMARK 999 DENSITY WITH ANY CERTAINTY, THUS THE DNA HAS BEEN MODELLED AS THE REMARK 999 PHOSPHATE BACKBONE ONLY AND RESIDUES ARE NOT ASSIGNED (ALL ARE REMARK 999 GIVEN AS ADENOSINE). THIS DNA IS THOUGHT TO BE A CRYSTALLOGRAPHIC REMARK 999 ARTEFACT AND NOT TO BE PHYSIOLOGICALLY RELEVANT. DBREF 2XHB A 1 757 UNP P56689 DPOL_THEGO 1 773 DBREF 2XHB D 0 27 PDB 2XHB 2XHB 0 27 DBREF 2XHB E 1 9 PDB 2XHB 2XHB 1 9 SEQADV 2XHB ALA A 215 UNP 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 VAL 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 GLU 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 LYS 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 SEQRES 1 D 28 DA DA DI DG DG DA DG DA DC DA DC DG DG SEQRES 2 D 28 DC DT DT DT DT DG DC DC DG DT DG DT DC SEQRES 3 D 28 DT DC SEQRES 1 E 9 DA DA DA DA DA DA DA DA DA HET NA A1758 1 HETNAM NA SODIUM ION FORMUL 4 NA NA 1+ FORMUL 5 HOH *22(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 GLY A 227 1 14 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 SER A 407 HIS A 416 1 10 HELIX 14 14 SER A 419 THR A 422 5 4 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 LEU A 571 1 20 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 GLY A 677 ARG A 689 1 13 HELIX 25 25 ARG A 709 ARG A 713 1 5 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 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 LYS A 74 0 SHEET 2 AB 4 PRO A 79 TYR A 86 -1 O ILE A 80 N LYS A 73 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 GLY A 167 THR A 172 1 O VAL A 170 N ASP A 182 SHEET 3 AD 6 ILE A 157 ASP A 164 -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 ALA A 539 0 SHEET 2 AF 6 GLY A 543 THR A 547 -1 O PHE A 545 N LEU A 537 SHEET 3 AF 6 TRP A 397 ASP A 404 -1 O VAL A 401 N ALA A 546 SHEET 4 AF 6 GLU A 578 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 506 CYS A 509 1555 1555 2.05 LINK O LYS A 101 NA NA A1758 1555 1555 2.45 LINK O HIS A 103 NA NA A1758 1555 1555 2.28 LINK O VAL A 106 NA NA A1758 1555 1555 2.32 LINK NA NA A1758 O HOH A2005 1555 1555 2.33 LINK NA NA A1758 O HOH A2006 1555 1555 2.71 SITE 1 AC1 5 LYS A 101 HIS A 103 VAL A 106 HOH A2005 SITE 2 AC1 5 HOH A2006 CRYST1 79.450 98.370 116.630 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 0.012587 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008574 0.00000