10 20 30 40 50 60 70 80 1NK8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 02-JAN-03 1NK8
TITLE A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A TITLE 2 GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER TITLE 3 EXTENSION, FOLLOWING INCORPORATION OF DCTP.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMER STRAND; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA TEMPLATE STRAND; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE I; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: BACILLUS FRAGMENT (ANALOGOUS TO THE E. COLI COMPND 13 KLENOW FRAGMENT); COMPND 14 EC: 2.7.7.7; COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 7 ORGANISM_TAXID: 1422; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET-30A(+)
KEYWDS DNA POLYMERASE I, DNA REPLICATION, KLENOW FRAGMENT, PROTEIN- KEYWDS 2 DNA COMPLEX, DNA MISMATCH, TRANSFERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.J.JOHNSON,L.S.BEESE
REVDAT 2 24-FEB-09 1NK8 1 VERSN REVDAT 1 30-MAR-04 1NK8 0
JRNL AUTH S.J.JOHNSON,L.S.BEESE JRNL TITL STRUCTURES OF MISMATCH REPLICATION ERRORS OBSERVED JRNL TITL 2 IN A DNA POLYMERASE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 116 803 2004 JRNL REFN ISSN 0092-8674 JRNL PMID 15035983 JRNL DOI 10.1016/S0092-8674(04)00252-1
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.J.JOHNSON,J.S.TAYLOR,L.S.BEESE REMARK 1 TITL PROCESSIVE DNA SYNTHESIS OBSERVED IN A POLYMERASE REMARK 1 TITL 2 CRYSTAL SUGGESTS A MECHANISM FOR THE PREVENTION OF REMARK 1 TITL 3 FRAMESHIFT MUTATIONS. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 100 3895 2003 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 12649320 REMARK 1 DOI 10.1073/PNAS.0630532100 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.R.KIEFER,C.MAO,J.C.BRAMAN,L.S.BEESE REMARK 1 TITL VISUALIZING DNA REPLICATION IN A CATALYTICALLY REMARK 1 TITL 2 ACTIVE BACILLUS DNA POLYMERASE CRYSTAL REMARK 1 REF NATURE V. 391 304 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/34693 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.R.KIEFER,C.MAO,C.J.HANSEN,S.L.BASEHORE, REMARK 1 AUTH 2 H.H.HOGREFE,J.C.BRAMAN,L.S.BEESE REMARK 1 TITL CRYSTAL STRUCTURE OF A THERMOSTABLE BACILLUS DNA REMARK 1 TITL 2 POLYMERASE I LARGE FRAGMENT AT 2.1 A RESOLUTION REMARK 1 REF STRUCTURE V. 5 95 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(97)00169-X
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2209622.770 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 60471 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 SET) : 0.190 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3048 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3081 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 159 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4650 REMARK 3 NUCLEIC ACID ATOMS : 465 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 532 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.99000 REMARK 3 B22 (A**2) : -3.87000 REMARK 3 B33 (A**2) : -2.12000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.90 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.370 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 44.12 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA-MULTI-ENDO.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : SUCROSE.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-MULTI-ENDO.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : SUCROSE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE BACILLUS POLYMERASE WAS CO- REMARK 3 CRYSTALLIZED WITH A DNA CONTAINING A 10 BASE PAIR DUPLEX AND A REMARK 3 5 BASE 5' TEMPLATE OVERHANG. THE CRYSTAL WAS SUBSEQUENTLY REMARK 3 PLACED INTO A STABILIZING SOLUTION CONTAINING DCTP. THE REMARK 3 RESULTING PRODUCT COMPLEX CONTAINED 11 BASE PAIRS OF DUPLEX REMARK 3 DNA AND A 4 BASE 5' TEMPLATE OVERHANG. THE LAST THREE BASES IN REMARK 3 THE OVERHANG ARE DISORDERED AND ARE NOT INCLUDED IN THE MODEL. REMARK 3 A 3' PHOSPHATE WAS LOCATED ON THE TEMPLATE STRAND (CHAIN C) TO REMARK 3 ENSURE THAT THE DNA DUPLEX WAS NOT BOUND BACKWARDS BY THE REMARK 3 POLYMERASE DURING CRYSTALLIZATION. ELECTRON DENSITY WAS REMARK 3 OBSERVED FOR ALL PROTEIN SIDE CHAINS EXCEPT LYSINE 298, WHICH REMARK 3 WAS MODELLED TO THE BETA CARBON. THE MAGNESIUM AT POSITION 901 REMARK 3 WAS ASSIGNED DUE TO THE LOW REFINED B-FACTOR AND COMPARISON REMARK 3 WITH A RELATED KLENTAQ POLYMERASE STRUCTURE (3KTQ). HOWEVER, REMARK 3 THE RESOLUTION OF THE STRUCTURE PREVENTS A DEFINITIVE REMARK 3 ASSIGNMENT BETWEEN WATER AND MAGNESIUM.
REMARK 4 REMARK 4 1NK8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB017944.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64853 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 26.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2BDP REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM REMARK 280 SULFATE, MPD, MES, PH 5.80, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 43.86150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.63950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.78950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.63950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.86150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.78950 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: EXISTS AS A MONOMER. ONE MOLECULE PER ASYMMETRIC UNIT.
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 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 400 REMARK 400 COMPOUND REMARK 400 THE POLYMERASE ADOPTS A DISTORTED OPEN CONFORMATION REMARK 400 WITH A GUANINE-THYMINE MISMATCH BOUND AT THE N-2 POSITION. REMARK 400 THE MISMATCH ADOPTS A WOBBLE CONFORMATION.
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 C 0 REMARK 465 DT C 1 REMARK 465 DA C 2
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 3 P OP1 OP2 REMARK 470 LYS A 298 CG CD CE NZ
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 298 154.51 -44.89 REMARK 500 ASP A 372 62.06 64.16 REMARK 500 ASP A 402 94.53 -165.11 REMARK 500 ALA A 421 42.08 -85.14 REMARK 500 LEU A 477 -70.97 -116.46 REMARK 500 ILE A 588 -63.39 -101.68 REMARK 500 LEU A 610 -59.93 -122.62 REMARK 500 ILE A 628 -28.46 -156.31 REMARK 500 HIS A 829 -56.19 70.80 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2639 DISTANCE = 10.24 ANGSTROMS REMARK 525 HOH A3058 DISTANCE = 8.10 ANGSTROMS
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 909 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 654 O REMARK 620 2 ASP A 830 OD2 76.2 REMARK 620 3 HOH A2801 O 78.1 103.5 REMARK 620 4 ASP A 653 OD2 77.0 125.7 115.7 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SUC A 901 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SUC A 902 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SUC A 903 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 910 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 911 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 912 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 909
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NJW RELATED DB: PDB REMARK 900 GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NJX RELATED DB: PDB REMARK 900 THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NJY RELATED DB: PDB REMARK 900 THYMINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NJZ RELATED DB: PDB REMARK 900 CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK0 RELATED DB: PDB REMARK 900 ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK4 RELATED DB: PDB REMARK 900 GUANINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK5 RELATED DB: PDB REMARK 900 ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK6 RELATED DB: PDB REMARK 900 CYTOSINE-CYTOSINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK7 RELATED DB: PDB REMARK 900 GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK9 RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A REMARK 900 GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER REMARK 900 EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. REMARK 900 RELATED ID: 1NKB RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A REMARK 900 GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER REMARK 900 EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. REMARK 900 RELATED ID: 1NKC RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A REMARK 900 GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER REMARK 900 EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND REMARK 900 DATP. REMARK 900 RELATED ID: 1NKE RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A REMARK 900 CYTOSINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER REMARK 900 EXTENSION, FOLLOWING INCORPORATION OF DCTP.
DBREF 1NK8 B 19 29 PDB 1NK8 1NK8 19 29 DBREF 1NK8 C 0 14 PDB 1NK8 1NK8 0 14 DBREF 1NK8 A 304 876 UNP P52026 DPO1_BACST 304 876
SEQRES 1 B 11 DG DC DG DA DT DC DA DG DC DG DC SEQRES 1 C 15 DG DT DA DC DG DT DG DC DT DG DA DT DC SEQRES 2 C 15 DG DC 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 ASP 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 CYS 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 TYR 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
HET SUC A 901 23 HET SUC A 902 23 HET SUC A 903 23 HET SO4 A 910 5 HET SO4 A 911 5 HET SO4 A 912 5 HET MG A 909 1
HETNAM SUC SUCROSE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION
FORMUL 4 SUC 3(C12 H22 O11) FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 MG MG 2+ FORMUL 11 HOH *532(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 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 LEU A 477 1 8 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 ILE A 588 1 20 HELIX 18 18 ILE A 588 VAL A 595 1 8 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 PHE A 690 1 11 HELIX 24 24 SER A 693 VAL A 697 5 5 HELIX 25 25 THR A 698 GLY A 715 1 18 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 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 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 ALA A 316 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 826 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 MG MG A 909 O TYR A 654 1555 1555 2.91 LINK MG MG A 909 OD2 ASP A 830 1555 1555 2.91 LINK MG MG A 909 O HOH A2801 1555 1555 2.93 LINK MG MG A 909 OD2 ASP A 653 1555 1555 2.82
CISPEP 1 GLU A 620 PRO A 621 0 -0.17
SITE 1 AC1 13 GLU A 325 TYR A 327 ASP A 372 ARG A 375 SITE 2 AC1 13 LEU A 395 ASP A 408 ILE A 605 ASN A 607 SITE 3 AC1 13 HOH A1031 HOH A1045 HOH A2121 HOH A3079 SITE 4 AC1 13 HOH C2845 SITE 1 AC2 11 GLU A 540 GLN A 543 TYR A 554 GLU A 751 SITE 2 AC2 11 GLN A 755 LYS A 758 ARG A 784 GLU A 788 SITE 3 AC2 11 HOH A2506 HOH A2932 HOH A3021 SITE 1 AC3 11 TYR A 519 PHE A 526 ASN A 527 ILE A 528 SITE 2 AC3 11 ASN A 529 TYR A 577 HOH A3073 HOH A3197 SITE 3 AC3 11 DA C 10 DT C 11 HOH C3074 SITE 1 AC4 4 MET A 299 ALA A 300 ARG A 343 ARG A 677 SITE 1 AC5 3 ARG A 702 LYS A 706 HOH A3083 SITE 1 AC6 4 HIS A 568 ARG A 779 ARG A 819 HOH A3042 SITE 1 AC7 4 ASP A 653 TYR A 654 ASP A 830 HOH A2801
CRYST1 87.723 93.579 105.279 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 0.011400 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010686 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009499 0.00000