PDB Short entry for 1NK6 HEADER TRANSFERASE/DNA 02-JAN-03 1NK6 TITLE CYTOSINE-CYTOSINE MISMATCH AT THE POLYMERASE ACTIVE SITE 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 KLENOW COMPND 13 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-DNA KEYWDS 2 COMPLEX, DNA MISMATCH, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.J.JOHNSON,L.S.BEESE REVDAT 4 16-AUG-23 1NK6 1 HETSYN REVDAT 3 29-JUL-20 1NK6 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 24-FEB-09 1NK6 1 VERSN REVDAT 1 30-MAR-04 1NK6 0 JRNL AUTH S.J.JOHNSON,L.S.BEESE JRNL TITL STRUCTURES OF MISMATCH REPLICATION ERRORS OBSERVED IN A DNA JRNL TITL 2 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 CRYSTAL REMARK 1 TITL 2 SUGGESTS A MECHANISM FOR THE PREVENTION OF FRAMESHIFT REMARK 1 TITL 3 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 ACTIVE REMARK 1 TITL 2 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,H.H.HOGREFE, REMARK 1 AUTH 2 J.C.BRAMAN,L.S.BEESE REMARK 1 TITL CRYSTAL STRUCTURE OF A THERMOSTABLE BACILLUS DNA POLYMERASE REMARK 1 TITL 2 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2697786.380 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 46660 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) : 0.213 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2374 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3634 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 200 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4650 REMARK 3 NUCLEIC ACID ATOMS : 365 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 306 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.38000 REMARK 3 B22 (A**2) : -3.85000 REMARK 3 B33 (A**2) : -4.53000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 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) : 0.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.890 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.020 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 43.58 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 9 BASE PAIR DUPLEX AND A 5 REMARK 3 BASE 5' TEMPLATE OVERHANG. THE FIVE OVERHANG BASES AND THE REMARK 3 ADJACENT TEMPLATE CYTOSINE FROM THE MISPAIR ARE ALL DISORDERED REMARK 3 AND ARE NOT INCLUDED IN THE MODEL. A SINGLE BASE 3' OVERHANG ON REMARK 3 THE TEMPLATE STRAND (CHAIN C) ASSURED THAT THE DNA DUPLEX WAS REMARK 3 NOT BOUND BACKWARDS BY THE POLYMERASE DURING CRYSTALLIZATION. REMARK 3 ELECTRON DENSITY WAS OBSERVED FOR ALL PROTEIN SIDE CHAINS EXCEPT REMARK 3 LYSINE 298, WHICH WAS MODELLED TO THE BETA CARBON. REMARK 4 REMARK 4 1NK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000017942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-00 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 : 51291 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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 (%): 56.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM SULFATE, REMARK 280 MPD, MES, PH 5.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 43.93150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.72600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.84100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.72600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.93150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.84100 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, D, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE POLYMERASE-DNA COMPLEX ADOPTS A DISTORTED OPEN REMARK 400 CONFORMATION WITH A FRAYED CYTOSINE-CYTOSINE MISMATCH REMARK 400 BOUND AT THE POLYMERASE INSERTION SITE (PRIMER STRAND) REMARK 400 AND EXCLUDED FROM THE ACTIVE SITE (TEMPLATE STRAND- REMARK 400 DISORDERED). 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 -2 REMARK 465 DA C -1 REMARK 465 DT C 0 REMARK 465 DC C 1 REMARK 465 DG C 2 REMARK 465 DC C 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 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 ASP A 402 91.97 -165.20 REMARK 500 ALA A 421 46.36 -87.42 REMARK 500 ALA A 433 13.24 -66.66 REMARK 500 ARG A 435 97.08 -65.36 REMARK 500 LEU A 477 -73.16 -113.76 REMARK 500 LEU A 610 -63.95 -122.79 REMARK 500 GLU A 620 70.02 39.04 REMARK 500 ILE A 628 -31.22 -155.18 REMARK 500 HIS A 829 -114.52 42.54 REMARK 500 REMARK 500 REMARK: NULL 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: 1NK7 RELATED DB: PDB REMARK 900 GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE REMARK 900 RELATED ID: 1NK8 RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE- REMARK 900 THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, REMARK 900 FOLLOWING INCORPORATION OF DCTP. REMARK 900 RELATED ID: 1NK9 RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE- REMARK 900 THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING REMARK 900 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 GUANINE- REMARK 900 THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING REMARK 900 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 GUANINE- REMARK 900 THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING REMARK 900 INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. REMARK 900 RELATED ID: 1NKE RELATED DB: PDB REMARK 900 A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A CYTOSINE- REMARK 900 THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, REMARK 900 FOLLOWING INCORPORATION OF DCTP. DBREF 1NK6 B 22 30 PDB 1NK6 1NK6 22 30 DBREF 1NK6 C -2 12 PDB 1NK6 1NK6 -2 12 DBREF 1NK6 A 304 876 UNP P52026 DPO1_BACST 304 876 SEQRES 1 B 9 DG DC DA DT DG DA DT DC DC SEQRES 1 C 15 DG DA DT DC DG DC DG DA DT DC DA DT DG SEQRES 2 C 15 DC DA 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 GLC D 1 11 HET FRU D 2 12 HET GLC E 1 11 HET FRU E 2 12 HET SO4 A 900 5 HET SO4 A 901 5 HET SO4 A 902 5 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 4 GLC 2(C6 H12 O6) FORMUL 4 FRU 2(C6 H12 O6) FORMUL 6 SO4 3(O4 S 2-) FORMUL 9 HOH *306(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 ASP A 409 MET A 416 1 8 HELIX 7 7 PRO A 424 GLY A 430 1 7 HELIX 8 8 LYS A 431 ARG A 435 5 5 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 GLU A 569 THR A 586 1 18 HELIX 16 16 TYR A 587 VAL A 595 1 9 HELIX 17 17 LEU A 630 LYS A 635 1 6 HELIX 18 18 ILE A 636 GLN A 638 5 3 HELIX 19 19 GLN A 656 GLU A 667 1 12 HELIX 20 20 ASP A 668 ARG A 677 1 10 HELIX 21 21 ASP A 680 PHE A 690 1 11 HELIX 22 22 SER A 693 VAL A 697 5 5 HELIX 23 23 THR A 698 GLY A 715 1 18 HELIX 24 24 SER A 717 ASN A 726 1 10 HELIX 25 25 SER A 728 PHE A 743 1 16 HELIX 26 26 PHE A 743 GLY A 761 1 19 HELIX 27 27 PRO A 774 SER A 778 5 5 HELIX 28 28 ASN A 780 GLU A 818 1 39 HELIX 29 29 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 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 VAL A 828 0 SHEET 2 D 4 GLU A 831 PRO A 837 -1 O GLU A 831 N VAL A 828 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 GLY A 869 N ILE A 649 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 C1 GLC D 1 O2 FRU D 2 1555 1555 1.48 LINK C1 GLC E 1 O2 FRU E 2 1555 1555 1.48 CISPEP 1 GLU A 620 PRO A 621 0 -10.42 CRYST1 87.863 93.682 105.452 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 0.011381 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010674 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009483 0.00000