HEADER TRANSFERASE/DNA 19-FEB-12 4DSK TITLE CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS TITLE 2 STEAROTHERMOPHILUS WITH DUPLEX DNA, PPI AND CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*CP*G)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*TP*CP*AP*CP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA POLYMERASE; COMPND 12 CHAIN: A; COMPND 13 FRAGMENT: RESIDUES 298-876; COMPND 14 EC: 2.7.7.7; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 9 ORGANISM_TAXID: 1422; SOURCE 10 GENE: DPO1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS DNA POLYMERASE, POLYMERIZATION FIDELITY, PYROPHOSPHOROLYSIS, PURINE KEYWDS 2 SELECTIVITY, BLUNT END EXTENSION, BASE STACKING, DNA SYNTHESIS, KEYWDS 3 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.GAN,R.ABDUR,H.H.LIU,J.SHENG,J.CATON-WILLIANS,A.S.SOARES,Z.HUANG REVDAT 2 13-SEP-23 4DSK 1 REMARK SEQADV LINK REVDAT 1 27-MAR-13 4DSK 0 JRNL AUTH J.H.GAN,R.ABDUR,H.H.LIU,J.SHENG,J.CATON-WILLIANS,A.S.SOARES, JRNL AUTH 2 Z.HUANG JRNL TITL BIOCHEMICAL AND STRUCTURAL INSIGHTS INTO THE FIDELITY OF JRNL TITL 2 BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 39669 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4433 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) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2237 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 273 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4617 REMARK 3 NUCLEIC ACID ATOMS : 497 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.87000 REMARK 3 B22 (A**2) : -1.11000 REMARK 3 B33 (A**2) : -0.77000 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): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.453 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5307 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7286 ; 1.758 ; 2.095 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 585 ; 5.919 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 236 ;38.030 ;24.280 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 878 ;17.744 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;18.785 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 816 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3841 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2892 ; 0.896 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4672 ; 1.767 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2415 ; 2.988 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2608 ; 4.807 ; 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 : 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 REMARK 4 REMARK 4 4DSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44295 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 70.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 3HT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE (PH 6.5), 18% V/V PEG8000, VAPOR DIFFUSION, SITTING REMARK 280 DROP 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 43.34600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.18150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.66950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.18150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.34600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.66950 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: 5710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 DG B 1 REMARK 465 DG B 2 REMARK 465 DC B 3 REMARK 465 DT B 4 REMARK 465 DT C 1 REMARK 465 DC C 17 REMARK 465 LYS A 549 REMARK 465 THR A 550 REMARK 465 LYS A 551 REMARK 465 THR A 552 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 DC C 16 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC C 16 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC C 16 C6 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 DG B 14 O3' DG B 14 C3' -0.045 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 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 5 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 10 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DA B 10 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 DT B 12 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 12 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT B 12 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC B 13 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 14 C5 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG C 7 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA C 14 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG C 15 O4' - C1' - N9 ANGL. DEV. = 7.7 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 ALA A 421 37.99 -85.49 REMARK 500 LYS A 431 -99.36 -97.86 REMARK 500 ILE A 588 -71.59 -102.46 REMARK 500 ILE A 628 -24.40 -150.53 REMARK 500 HIS A 829 -73.73 72.69 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 CA B 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 14 OP1 REMARK 620 2 HOH B 201 O 95.2 REMARK 620 3 POP A1001 O 147.5 112.1 REMARK 620 4 POP A1001 O2 103.1 91.5 60.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1004 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 354 OD1 REMARK 620 2 GLN A 356 OE1 109.7 REMARK 620 3 HOH A1112 O 143.0 106.5 REMARK 620 4 HOH A1342 O 77.1 108.0 85.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 830 OD1 REMARK 620 2 GLU A 831 OE2 116.1 REMARK 620 3 POP A1001 O 122.5 120.3 REMARK 620 4 POP A1001 O5 130.1 97.8 51.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 858 O REMARK 620 2 HOH A1186 O 75.9 REMARK 620 3 HOH A1240 O 77.4 112.7 REMARK 620 4 HOH A1257 O 142.3 90.0 76.3 REMARK 620 5 HOH A1367 O 75.1 136.0 92.1 132.1 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 CA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS REMARK 900 STEAROTHERMOPHILUS V713P MUTANT BOUND TO G:DCTP REMARK 900 RELATED ID: 4DSI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS REMARK 900 STEAROTHERMOPHILUS WUTH DUPLEX DNA, SE-DGTP AND CALCIUM REMARK 900 RELATED ID: 4DSJ RELATED DB: PDB REMARK 900 DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS WUTH DUPLEX DNA, REMARK 900 DGTP AND CALCIUM REMARK 900 RELATED ID: 4DSL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS REMARK 900 STEAROTHERMOPHILUS WITH DUPLEX DNA AND CALCIUM DBREF 4DSK A 298 876 UNP D9N168 D9N168_GEOSE 1 579 DBREF 4DSK B 1 14 PDB 4DSK 4DSK 1 14 DBREF 4DSK C 1 17 PDB 4DSK 4DSK 1 17 SEQADV 4DSK ASP A 598 UNP D9N168 ALA 301 ENGINEERED MUTATION SEQADV 4DSK VAL A 713 UNP D9N168 PRO 416 ENGINEERED MUTATION SEQRES 1 B 14 DG DG DC DT DA DC DA DG DG DA DC DT DC SEQRES 2 B 14 DG SEQRES 1 C 17 DT DC DA DC DG DA DG DT DC DC DT DG DT SEQRES 2 C 17 DA DG DC DC SEQRES 1 A 579 LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU GLU SEQRES 2 A 579 MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL VAL SEQRES 3 A 579 GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE ALA SEQRES 4 A 579 VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO GLU SEQRES 5 A 579 THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU GLY SEQRES 6 A 579 ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS ARG SEQRES 7 A 579 ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU CYS SEQRES 8 A 579 GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU LEU SEQRES 9 A 579 ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA ALA SEQRES 10 A 579 LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU ALA SEQRES 11 A 579 VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP GLU SEQRES 12 A 579 PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA ALA SEQRES 13 A 579 ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU ARG SEQRES 14 A 579 ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU GLN SEQRES 15 A 579 PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA GLY SEQRES 16 A 579 VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY LYS SEQRES 17 A 579 GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG ILE SEQRES 18 A 579 TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER PRO SEQRES 19 A 579 LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN LEU SEQRES 20 A 579 PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SER SEQRES 21 A 579 ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU ILE SEQRES 22 A 579 VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS LEU SEQRES 23 A 579 GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL ARG SEQRES 24 A 579 PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN ALA SEQRES 25 A 579 LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO ASN SEQRES 26 A 579 LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG LYS SEQRES 27 A 579 ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP LEU SEQRES 28 A 579 ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG VAL SEQRES 29 A 579 LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU ALA SEQRES 30 A 579 PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA MET SEQRES 31 A 579 ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO ASN SEQRES 32 A 579 MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE VAL SEQRES 33 A 579 TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU ASN SEQRES 34 A 579 ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG TYR SEQRES 35 A 579 PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU ASN SEQRES 36 A 579 ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR THR SEQRES 37 A 579 LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SER SEQRES 38 A 579 ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET ALA SEQRES 39 A 579 MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE ILE SEQRES 40 A 579 LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS GLU SEQRES 41 A 579 GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS ASP SEQRES 42 A 579 GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU ARG SEQRES 43 A 579 LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA VAL SEQRES 44 A 579 THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR GLY SEQRES 45 A 579 SER THR TRP TYR ASP ALA LYS HET CA B 101 1 HET POP A1001 9 HET CA A1002 1 HET CA A1003 1 HET CA A1004 1 HETNAM CA CALCIUM ION HETNAM POP PYROPHOSPHATE 2- FORMUL 4 CA 4(CA 2+) FORMUL 5 POP H2 O7 P2 2- FORMUL 9 HOH *300(H2 O) HELIX 1 1 THR A 308 ALA A 313 5 6 HELIX 2 2 ARG A 347 LEU A 352 1 6 HELIX 3 3 ASP A 354 GLY A 362 1 9 HELIX 4 4 ASP A 372 LYS A 383 1 12 HELIX 5 5 LEU A 394 ASP A 402 1 9 HELIX 6 6 PRO A 403 GLY A 406 5 4 HELIX 7 7 ASP A 409 MET A 416 1 8 HELIX 8 8 PRO A 424 GLY A 430 1 7 HELIX 9 9 ASP A 439 ASN A 468 1 30 HELIX 10 10 GLN A 470 LEU A 477 1 8 HELIX 11 11 LEU A 477 GLY A 492 1 16 HELIX 12 12 ASP A 496 GLY A 523 1 28 HELIX 13 13 SER A 530 GLU A 540 1 11 HELIX 14 14 SER A 557 ALA A 565 1 9 HELIX 15 15 PRO A 566 HIS A 568 5 3 HELIX 16 16 GLU A 569 ILE A 588 1 20 HELIX 17 17 ILE A 588 VAL A 595 1 8 HELIX 18 18 LEU A 630 LYS A 635 1 6 HELIX 19 19 ILE A 636 GLN A 638 5 3 HELIX 20 20 GLN A 656 GLU A 667 1 12 HELIX 21 21 ASP A 668 ARG A 677 1 10 HELIX 22 22 ASP A 680 GLN A 691 1 12 HELIX 23 23 SER A 693 VAL A 697 5 5 HELIX 24 24 THR A 698 GLY A 715 1 18 HELIX 25 25 SER A 717 ASN A 726 1 10 HELIX 26 26 SER A 728 PHE A 743 1 16 HELIX 27 27 PHE A 743 GLY A 761 1 19 HELIX 28 28 PRO A 774 SER A 778 5 5 HELIX 29 29 ASN A 780 GLU A 818 1 39 HELIX 30 30 GLU A 840 ALA A 855 1 16 SHEET 1 A 6 THR A 302 LEU A 303 0 SHEET 2 A 6 GLY A 342 LEU A 346 1 O PHE A 345 N THR A 302 SHEET 3 A 6 GLY A 334 ASN A 339 -1 N VAL A 337 O PHE A 344 SHEET 4 A 6 LYS A 315 GLU A 321 -1 N ALA A 317 O VAL A 338 SHEET 5 A 6 LYS A 367 MET A 370 1 O SER A 369 N LEU A 318 SHEET 6 A 6 VAL A 390 ASP A 393 1 O PHE A 392 N MET A 370 SHEET 1 B 3 LYS A 601 VAL A 602 0 SHEET 2 B 3 VAL A 493 VAL A 495 -1 N VAL A 493 O VAL A 602 SHEET 3 B 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 C 2 ILE A 605 ASN A 607 0 SHEET 2 C 2 SER A 617 THR A 619 -1 O THR A 619 N ILE A 605 SHEET 1 D 4 HIS A 823 GLN A 827 0 SHEET 2 D 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 D 4 TRP A 647 TYR A 654 -1 N LEU A 648 O ALA A 836 SHEET 4 D 4 VAL A 864 GLY A 869 -1 O HIS A 867 N ALA A 651 SHEET 1 E 2 TYR A 762 THR A 764 0 SHEET 2 E 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 LINK OP1 DG B 14 CA CA B 101 1555 1555 2.51 LINK CA CA B 101 O HOH B 201 1555 1555 2.29 LINK CA CA B 101 O POP A1001 1555 1555 2.33 LINK CA CA B 101 O2 POP A1001 1555 1555 2.71 LINK OD1 ASP A 354 CA CA A1004 1555 1555 2.58 LINK OE1 GLN A 356 CA CA A1004 1555 1555 2.97 LINK OD1 ASP A 830 CA CA A1002 1555 1555 2.45 LINK OE2 GLU A 831 CA CA A1002 1555 1555 2.76 LINK O LEU A 858 CA CA A1003 1555 1555 2.77 LINK O POP A1001 CA CA A1002 1555 1555 2.81 LINK O5 POP A1001 CA CA A1002 1555 1555 3.03 LINK CA CA A1003 O HOH A1186 1555 1555 2.66 LINK CA CA A1003 O HOH A1240 1555 1555 2.62 LINK CA CA A1003 O HOH A1257 1555 1555 2.48 LINK CA CA A1003 O HOH A1367 1555 1555 2.61 LINK CA CA A1004 O HOH A1112 1555 1555 2.28 LINK CA CA A1004 O HOH A1342 1555 1555 2.44 CISPEP 1 GLU A 620 PRO A 621 0 2.25 SITE 1 AC1 4 POP A1001 CA A1002 DG B 14 HOH B 201 SITE 1 AC2 7 ASP A 653 TYR A 654 ASP A 830 CA A1002 SITE 2 AC2 7 HOH A1222 DG B 14 CA B 101 SITE 1 AC3 5 ASP A 830 GLU A 831 POP A1001 DG B 14 SITE 2 AC3 5 CA B 101 SITE 1 AC4 5 LEU A 858 HOH A1186 HOH A1240 HOH A1257 SITE 2 AC4 5 HOH A1367 SITE 1 AC5 4 ASP A 354 GLN A 356 HOH A1112 HOH A1342 CRYST1 86.692 93.339 106.363 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 0.011535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009402 0.00000