HEADER TRANSFERASE/DNA 19-FEB-12 4DSI TITLE CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS TITLE 2 STEAROTHERMOPHILUS WITH DUPLEX DNA, SE-DGTP AND CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 298-876; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: SE-DGTP; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: DPO1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHESIZED DNA; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SE-MODIFIED DGTP KEYWDS DNA POLYMERASE, POLYMERIZATION FIDELITY, CALCIUM CATION, 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 1 27-MAR-13 4DSI 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. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 51429 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2753 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3378 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 213 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4659 REMARK 3 NUCLEIC ACID ATOMS : 366 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.18000 REMARK 3 B22 (A**2) : -0.77000 REMARK 3 B33 (A**2) : -1.41000 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.493 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5223 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7132 ; 1.800 ; 2.073 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 586 ; 6.293 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 231 ;34.891 ;24.156 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 884 ;18.190 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;21.156 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 796 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3785 ; 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): 2911 ; 0.918 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4700 ; 1.781 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2312 ; 2.980 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2429 ; 4.792 ; 4.500 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 4DSI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB070726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-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 : ALS REMARK 200 BEAMLINE : 8.2.2 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 : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54369 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 70.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33700 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB 3HT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M COBALT CHLORIDE, 0.1 M MES (PH REMARK 280 6.5), 1.8 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING 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 44.28650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.96400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.69350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.96400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.28650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.69350 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: 6360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 DA B 1 REMARK 465 DT B 2 REMARK 465 DC B 3 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 12 O3' DG B 12 C3' -0.071 REMARK 500 DT C 3 C5 DT C 3 C7 0.043 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 DG B 5 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 8 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DC B 9 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 10 C4' - C3' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DC B 9 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC C 2 OP1 - P - OP2 ANGL. DEV. = 10.9 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG C 9 O4' - C1' - N9 ANGL. DEV. = 4.3 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 402 93.07 -164.14 REMARK 500 ALA A 421 49.55 -80.73 REMARK 500 LYS A 431 -54.57 -124.29 REMARK 500 LEU A 477 -67.34 -121.74 REMARK 500 GLN A 524 157.95 175.12 REMARK 500 GLU A 540 -55.57 -124.58 REMARK 500 ILE A 588 -71.21 -96.87 REMARK 500 ILE A 628 -31.11 -139.45 REMARK 500 GLN A 691 59.73 39.88 REMARK 500 HIS A 829 -55.23 72.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 689 23.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DG C 101 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM REMARK 900 BACILLUS STEAROTHERMOPHILUS V713P MUTANT BOUND TO G:DCTP REMARK 900 RELATED ID: 4DSJ RELATED DB: PDB REMARK 900 DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS WUTH REMARK 900 DUPLEX DNA, DGTP AND CALCIUM REMARK 900 RELATED ID: 4DSK RELATED DB: PDB REMARK 900 DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS WUTH REMARK 900 DUPLEX DNA, PPI AND CALCIUM REMARK 900 RELATED ID: 4DSL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM REMARK 900 BACILLUS STEAROTHERMOPHILUS WITH DUPLEX DNA AND CALCIUM DBREF 4DSI A 298 876 UNP D9N168 D9N168_GEOSE 1 579 DBREF 4DSI B 1 12 PDB 4DSI 4DSI 1 12 DBREF 4DSI C 1 9 PDB 4DSI 4DSI 1 9 SEQADV 4DSI GLY A 296 UNP D9N168 EXPRESSION TAG SEQADV 4DSI SER A 297 UNP D9N168 EXPRESSION TAG SEQADV 4DSI ASP A 598 UNP D9N168 ALA 301 ENGINEERED MUTATION SEQADV 4DSI VAL A 713 UNP D9N168 PRO 416 ENGINEERED MUTATION SEQRES 1 A 581 GLY SER LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR SEQRES 2 A 581 GLU GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU SEQRES 3 A 581 VAL VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY SEQRES 4 A 581 ILE ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG SEQRES 5 A 581 PRO GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP SEQRES 6 A 581 LEU GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER SEQRES 7 A 581 LYS ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU SEQRES 8 A 581 LEU CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR SEQRES 9 A 581 LEU LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA SEQRES 10 A 581 ALA ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP SEQRES 11 A 581 GLU ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO SEQRES 12 A 581 ASP GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA SEQRES 13 A 581 ALA ALA ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU SEQRES 14 A 581 LEU ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU SEQRES 15 A 581 GLU GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE SEQRES 16 A 581 ALA GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET SEQRES 17 A 581 GLY LYS GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN SEQRES 18 A 581 ARG ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SEQRES 19 A 581 SER PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU SEQRES 20 A 581 GLN LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER SEQRES 21 A 581 THR SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS SEQRES 22 A 581 GLU ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY SEQRES 23 A 581 LYS LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL SEQRES 24 A 581 VAL ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN SEQRES 25 A 581 GLN ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU SEQRES 26 A 581 PRO ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY SEQRES 27 A 581 ARG LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP SEQRES 28 A 581 TRP LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU SEQRES 29 A 581 ARG VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET SEQRES 30 A 581 GLU ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR SEQRES 31 A 581 ALA MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR SEQRES 32 A 581 PRO ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY SEQRES 33 A 581 ILE VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN SEQRES 34 A 581 LEU ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU SEQRES 35 A 581 ARG TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET SEQRES 36 A 581 GLU ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL SEQRES 37 A 581 THR THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE SEQRES 38 A 581 THR SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG SEQRES 39 A 581 MET ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP SEQRES 40 A 581 ILE ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU SEQRES 41 A 581 LYS GLU GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL SEQRES 42 A 581 HIS ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET SEQRES 43 A 581 GLU ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN SEQRES 44 A 581 ALA VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS SEQRES 45 A 581 TYR GLY SER THR TRP TYR ASP ALA LYS SEQRES 1 B 12 DA DT DC DC DG DA DG DT DC DA DG DG SEQRES 1 C 9 DC DC DT DG DA DC DT DC DG HET GOL A 901 6 HET GOL A 902 6 HET GOL A 903 6 HET GOL A 904 6 HET GOL A 905 6 HET SO4 A 906 5 HET SO4 A 907 5 HET SO4 A 908 5 HET DG C 101 12 HET CA C 102 1 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM DG 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 SO4 3(O4 S 2-) FORMUL 12 DG C10 H14 N5 O7 P FORMUL 13 CA CA 2+ FORMUL 14 HOH *242(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 ASP A 363 1 10 HELIX 4 4 ASP A 372 TRP A 382 1 11 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 ALA A 522 1 27 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 ILE A 712 1 15 HELIX 25 25 VAL A 713 GLY A 715 5 3 HELIX 26 26 SER A 717 ASN A 726 1 10 HELIX 27 27 SER A 728 PHE A 743 1 16 HELIX 28 28 PHE A 743 GLY A 761 1 19 HELIX 29 29 PRO A 774 SER A 778 5 5 HELIX 30 30 ASN A 780 ARG A 819 1 40 HELIX 31 31 GLU A 840 ALA A 855 1 16 HELIX 32 32 THR A 871 ALA A 875 5 5 SHEET 1 A 6 THR A 302 LEU A 303 0 SHEET 2 A 6 GLY A 342 LEU A 346 1 O ARG A 343 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 SER A 617 N ASN A 607 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 PHE A 650 O LEU A 834 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 DC C 8 CA CA C 102 1555 1555 2.21 CISPEP 1 GLU A 620 PRO A 621 0 0.72 SITE 1 AC1 9 GLU A 321 PHE A 371 ARG A 375 ASP A 409 SITE 2 AC1 9 VAL A 410 ASP A 425 LYS A 450 HOH A1154 SITE 3 AC1 9 HOH A1198 SITE 1 AC2 8 THR A 586 TYR A 587 LEU A 591 PRO A 621 SITE 2 AC2 8 ASN A 622 ASN A 625 HOH A1080 DA C 5 SITE 1 AC3 4 TRP A 382 PHE A 490 ALA A 491 LYS A 601 SITE 1 AC4 8 TYR A 327 ASP A 372 LYS A 374 PHE A 606 SITE 2 AC4 8 ASN A 607 GLN A 608 HOH A1027 HOH A1043 SITE 1 AC5 4 GLY A 715 ILE A 716 PHE A 740 MET A 750 SITE 1 AC6 4 MET A 299 ALA A 300 ARG A 343 ARG A 677 SITE 1 AC7 5 TYR A 714 PHE A 786 ARG A 789 HOH A1085 SITE 2 AC7 5 DC C 1 SITE 1 AC8 4 HIS A 682 ARG A 702 LYS A 706 HOH A1158 SITE 1 AC9 2 DC B 4 DG C 9 SITE 1 BC1 4 ASN A 527 ASN A 529 DT C 7 DC C 8 CRYST1 88.573 93.387 105.928 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 0.011290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009440 0.00000 MASTER 398 0 10 32 17 0 15 6 0 0 0 47 END