HEADER TRANSFERASE/DNA 04-JUN-09 3HPO TITLE CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS TITLE 2 STEAROTHERMOPHILUS Y714S MUTANT BOUND TO G:T MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, LARGE FRAGMENT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 297-876; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(P*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'; 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: PET30A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE PRIMER STRAND; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE TEMPLATE STRAND KEYWDS PROTEIN-DNA COMPLEX, DNA POLYMERASE I, DNA REPLICATION, DNA-BINDING, KEYWDS 2 DNA-DIRECTED DNA POLYMERASE, HYDROLASE, NUCLEASE, KEYWDS 3 NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.Y.WU,L.S.BEESE REVDAT 6 06-SEP-23 3HPO 1 REMARK REVDAT 5 13-OCT-21 3HPO 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3HPO 1 COMPND REMARK DBREF HET REVDAT 4 2 1 HETNAM FORMUL LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 01-NOV-17 3HPO 1 REMARK REVDAT 2 29-JUN-11 3HPO 1 JRNL REVDAT 1 23-JUN-10 3HPO 0 JRNL AUTH E.Y.WU,L.S.BEESE JRNL TITL THE STRUCTURE OF A HIGH FIDELITY DNA POLYMERASE BOUND TO A JRNL TITL 2 MISMATCHED NUCLEOTIDE REVEALS AN "AJAR" INTERMEDIATE JRNL TITL 3 CONFORMATION IN THE NUCLEOTIDE SELECTION MECHANISM. JRNL REF J.BIOL.CHEM. V. 286 19758 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21454515 JRNL DOI 10.1074/JBC.M110.191130 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 83554 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4178 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5002 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4649 REMARK 3 NUCLEIC ACID ATOMS : 387 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 724 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.400 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5258 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7203 ; 1.170 ; 2.081 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 590 ; 5.022 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;32.559 ;24.261 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 881 ;13.839 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;14.502 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 812 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3798 ; 0.004 ; 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): 2921 ; 0.584 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4717 ; 1.134 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2337 ; 1.820 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2482 ; 2.990 ; 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. REMARK 4 REMARK 4 3HPO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83554 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 45.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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 ENTRY 1L3U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% SATURATED AMMONIUM SULFATE, 0.1M REMARK 280 MES, 2.5% V/V METHYLPENTANEDIOL, 10MM MAGNESIUM SULFATE, PH 5.8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 45.10500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.75500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.86500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.75500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.10500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.86500 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 300 REMARK: THE BIOLOGICAL UNIT IS A COMPLEX OF ENZYME AND DNA. THE REMARK 300 ASYMMETRIC UNIT IS THE SAME AS THE BIOLOGICAL ASSEMBLY. 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: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASN A 670 O HOH A 897 2.10 REMARK 500 O HOH A 982 O HOH A 1149 2.19 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 DC B 25 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 26 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 27 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DC B 27 C4' - C3' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT C 10 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 298 142.25 -32.37 REMARK 500 ASP A 372 62.54 61.92 REMARK 500 ASP A 402 97.74 -165.27 REMARK 500 ALA A 421 39.15 -84.23 REMARK 500 ALA A 436 147.72 -176.27 REMARK 500 LEU A 477 -70.23 -118.45 REMARK 500 TYR A 587 -60.51 -97.36 REMARK 500 LEU A 610 -53.99 -125.31 REMARK 500 ILE A 628 -29.76 -150.57 REMARK 500 HIS A 768 18.47 81.44 REMARK 500 HIS A 829 -54.02 75.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 83 O REMARK 620 2 HOH A 157 O 87.2 REMARK 620 3 TTP A 201 O2A 172.9 94.9 REMARK 620 4 TTP A 201 O2B 91.8 176.4 86.5 REMARK 620 5 TTP A 201 O2G 85.1 94.4 87.9 89.0 REMARK 620 6 HOH A 894 O 90.2 88.9 96.6 87.7 174.2 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HP6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACILLUS FRAGMENT DNA POLYMERASE I F710Y REMARK 900 MUTANT IN AJAR CONFORMATION BOUND TO G:T MISMATCH REMARK 900 RELATED ID: 3HT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACILLUS FRAGMENT DNA POLYMERASE I V713P REMARK 900 MUTANT BOUND TO G:DCTP DBREF 3HPO A 297 876 PDB 3HPO 3HPO 297 876 DBREF 3HPO B 21 29 PDB 3HPO 3HPO 21 29 DBREF 3HPO C 3 12 PDB 3HPO 3HPO 3 12 SEQADV 3HPO ALA A 329 PDB 3HPO ASP 329 ENGINEERED MUTATION SEQADV 3HPO SER A 714 PDB 3HPO TYR 714 ENGINEERED MUTATION SEQRES 1 A 580 ALA LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU SEQRES 2 A 580 GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL SEQRES 3 A 580 VAL GLU GLU ASN TYR HIS ALA ALA PRO ILE VAL GLY ILE SEQRES 4 A 580 ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO SEQRES 5 A 580 GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU SEQRES 6 A 580 GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS SEQRES 7 A 580 ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU SEQRES 8 A 580 CME GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU SEQRES 9 A 580 LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA SEQRES 10 A 580 ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU SEQRES 11 A 580 ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP SEQRES 12 A 580 GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA SEQRES 13 A 580 ALA ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU SEQRES 14 A 580 ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU SEQRES 15 A 580 GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA SEQRES 16 A 580 GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY SEQRES 17 A 580 LYS GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG SEQRES 18 A 580 ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER SEQRES 19 A 580 PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN SEQRES 20 A 580 LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SEQRES 21 A 580 SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU SEQRES 22 A 580 ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS SEQRES 23 A 580 LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL SEQRES 24 A 580 ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN SEQRES 25 A 580 ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO SEQRES 26 A 580 ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG SEQRES 27 A 580 LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP SEQRES 28 A 580 LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG SEQRES 29 A 580 VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU SEQRES 30 A 580 ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA SEQRES 31 A 580 MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO SEQRES 32 A 580 ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE SEQRES 33 A 580 VAL SER GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU SEQRES 34 A 580 ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG SEQRES 35 A 580 TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU SEQRES 36 A 580 ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR SEQRES 37 A 580 THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SEQRES 38 A 580 SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET SEQRES 39 A 580 ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE SEQRES 40 A 580 ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS SEQRES 41 A 580 GLU GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS SEQRES 42 A 580 ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU SEQRES 43 A 580 ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA SEQRES 44 A 580 VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR SEQRES 45 A 580 GLY SER THR TRP TYR ASP ALA LYS SEQRES 1 B 9 DC DG DA DT DC DA DC DG DOC SEQRES 1 C 10 DG DG DC DG DT DG DA DT DC DG MODRES 3HPO CME A 388 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 3HPO DOC B 29 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET CME A 388 10 HET DOC B 29 18 HET GLC D 1 11 HET FRU D 2 12 HET MG A 200 1 HET TTP A 201 29 HET SO4 A 912 5 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM MG MAGNESIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 1 CME C5 H11 N O3 S2 FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 GLC C6 H12 O6 FORMUL 4 FRU C6 H12 O6 FORMUL 5 MG MG 2+ FORMUL 6 TTP C10 H17 N2 O14 P3 FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *724(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 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 LYS A 431 ARG A 435 5 5 HELIX 10 10 ASP A 439 ASN A 468 1 30 HELIX 11 11 GLN A 470 GLU A 476 1 7 HELIX 12 12 LEU A 477 GLY A 492 1 16 HELIX 13 13 ASP A 496 GLY A 523 1 28 HELIX 14 14 SER A 530 GLU A 540 1 11 HELIX 15 15 SER A 557 ALA A 565 1 9 HELIX 16 16 PRO A 566 HIS A 568 5 3 HELIX 17 17 GLU A 569 TYR A 587 1 19 HELIX 18 18 TYR A 587 VAL A 595 1 9 HELIX 19 19 LEU A 630 LYS A 635 1 6 HELIX 20 20 ILE A 636 GLN A 638 5 3 HELIX 21 21 GLN A 656 GLU A 667 1 12 HELIX 22 22 ASP A 668 ARG A 677 1 10 HELIX 23 23 ASP A 680 GLN A 691 1 12 HELIX 24 24 SER A 693 VAL A 697 5 5 HELIX 25 25 THR A 698 ILE A 712 1 15 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 GLU A 818 1 39 HELIX 31 31 GLU A 840 GLN A 854 1 15 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 PHE A 650 O LEU A 834 SHEET 4 D 4 VAL A 864 GLY A 869 -1 O ASP A 865 N ASP A 653 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 C LEU A 387 N CME A 388 1555 1555 1.33 LINK C CME A 388 N GLY A 389 1555 1555 1.33 LINK O3' DG B 28 P DOC B 29 1555 1555 1.59 LINK C1 GLC D 1 O2 FRU D 2 1555 1555 1.42 LINK O HOH A 83 MG MG A 200 1555 1555 2.01 LINK O HOH A 157 MG MG A 200 1555 1555 2.03 LINK MG MG A 200 O2A TTP A 201 1555 1555 1.98 LINK MG MG A 200 O2B TTP A 201 1555 1555 2.16 LINK MG MG A 200 O2G TTP A 201 1555 1555 1.98 LINK MG MG A 200 O HOH A 894 1555 1555 2.18 CISPEP 1 GLU A 620 PRO A 621 0 3.11 CRYST1 90.210 93.730 105.510 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 0.011085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009478 0.00000