PDB Short entry for 1IG9 HEADER TRANSFERASE/DNA 17-APR-01 1IG9 TITLE STRUCTURE OF THE REPLICATING COMPLEX OF A POL ALPHA FAMILY DNA TITLE 2 POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) COMPND 3 -3'; COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SUBSTRATE DNA, TEMPLATE STRAND; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*(DOC))-3'; COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: SUBSTRATE DNA, PRIMER STRAND (DIDEOXY-TERMINATED); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA POLYMERASE; COMPND 14 CHAIN: A; COMPND 15 EC: 2.7.7.7; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: 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: ENTEROBACTERIA PHAGE RB69; SOURCE 7 ORGANISM_TAXID: 12353; SOURCE 8 GENE: GP43; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PRB.43 EXO- KEYWDS DNA POLYMERASE, CATALYTIC COMPLEX, FIDELITY, TWO METAL ION MECHANISM, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.C.FRANKLIN,J.WANG,T.A.STEITZ REVDAT 4 16-AUG-23 1IG9 1 REMARK REVDAT 3 27-OCT-21 1IG9 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1IG9 1 VERSN REVDAT 1 11-JUN-01 1IG9 0 JRNL AUTH M.C.FRANKLIN,J.WANG,T.A.STEITZ JRNL TITL STRUCTURE OF THE REPLICATING COMPLEX OF A POL ALPHA FAMILY JRNL TITL 2 DNA POLYMERASE JRNL REF CELL(CAMBRIDGE,MASS.) V. 105 657 2001 JRNL REFN ISSN 0092-8674 JRNL PMID 11389835 JRNL DOI 10.1016/S0092-8674(01)00367-1 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.WANG,A.K.SATTAR,C.C.WANG,J.D.KARAM,W.H.KONIGSBERG, REMARK 1 AUTH 2 T.A.STEITZ REMARK 1 TITL CRYSTAL STRUCTURE OF A POL ALPHA FAMILY REPLICATION DNA REMARK 1 TITL 2 POLYMERASE FROM BACTERIOPHAGE RB69 REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 89 1087 1997 REMARK 1 REFN ISSN 0092-8674 REMARK 1 DOI 10.1016/S0092-8674(00)80296-2 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.SHAMOO,T.A.STEITZ REMARK 1 TITL BUILDING A REPLISOME FROM INTERACTING PIECES: SLIDING CLAMP REMARK 1 TITL 2 COMPLEXED TO A PEPTIDE FROM DNA POLYMERASE AND A POLYMERASE REMARK 1 TITL 3 EDITING COMPLEX REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 99 155 1999 REMARK 1 REFN ISSN 0092-8674 REMARK 1 DOI 10.1016/S0092-8674(00)81647-5 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 AND HUBER, AS IMPLEMENTED IN CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 297902.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 37266 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) : 0.197 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 3622 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1564 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 170 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7355 REMARK 3 NUCLEIC ACID ATOMS : 650 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 356 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.63000 REMARK 3 B22 (A**2) : -2.70000 REMARK 3 B33 (A**2) : 7.34000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.52 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) : 0.890 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) : 2.140 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.520 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.040 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.030 ; 5.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 48.16 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : TTP.PAR REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : TTP.TOP REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.25 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38733 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1CLQ, WITH NON-PROTEIN ATOMS REMOVED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 350 MONOMETHYL ETHER, CALCIUM REMARK 280 CHLORIDE, SODIUM CACODYLATE, PH 6.25, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K 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 40.39350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.99850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.30100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.99850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.39350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.30100 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: EACH MONOMER CONSTITUTES A FUNCTIONAL 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 APPLY THE FOLLOWING TO CHAINS: T, P, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 902 REMARK 465 PHE A 903 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 SER A 44 -71.51 -55.71 REMARK 500 GLN A 45 104.67 -41.95 REMARK 500 THR A 47 -155.86 -156.53 REMARK 500 PRO A 124 90.39 -59.08 REMARK 500 PRO A 155 0.37 -63.09 REMARK 500 PRO A 179 132.94 -32.17 REMARK 500 LYS A 208 60.48 -112.41 REMARK 500 PHE A 221 -75.13 -131.53 REMARK 500 LYS A 240 0.48 -65.88 REMARK 500 VAL A 252 -97.12 -79.88 REMARK 500 ILE A 253 90.12 67.84 REMARK 500 TYR A 257 46.16 -150.98 REMARK 500 ASN A 402 -178.62 175.94 REMARK 500 LYS A 405 -71.87 -52.81 REMARK 500 SER A 414 57.07 29.42 REMARK 500 LEU A 415 -79.87 -37.64 REMARK 500 ARG A 467 -175.81 -53.76 REMARK 500 ASP A 468 -71.30 -106.41 REMARK 500 LEU A 503 31.21 -77.72 REMARK 500 PRO A 506 100.21 -41.90 REMARK 500 LEU A 508 83.75 -67.44 REMARK 500 ASP A 511 -150.61 -131.61 REMARK 500 GLU A 512 127.80 -171.11 REMARK 500 ASP A 579 102.47 -171.53 REMARK 500 GLU A 607 -70.51 -67.77 REMARK 500 VAL A 608 -70.83 -49.07 REMARK 500 THR A 611 -179.25 -59.89 REMARK 500 THR A 622 -67.75 65.32 REMARK 500 ASP A 623 23.57 -141.08 REMARK 500 GLU A 638 93.27 -60.91 REMARK 500 SER A 639 -91.17 -139.02 REMARK 500 LYS A 640 44.88 -65.01 REMARK 500 GLU A 686 -86.50 -112.65 REMARK 500 VAL A 793 48.11 39.85 REMARK 500 ASN A 818 73.20 -51.67 REMARK 500 ILE A 819 93.68 -57.56 REMARK 500 ASP A 820 -30.20 -173.88 REMARK 500 GLU A 892 58.73 -116.74 REMARK 500 LYS A 893 -161.50 37.84 REMARK 500 ALA A 895 84.40 -57.41 REMARK 500 SER A 896 -22.15 -37.70 REMARK 500 LEU A 897 -27.97 67.10 REMARK 500 ASP A 899 -85.13 -38.24 REMARK 500 MET A 900 80.94 -61.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA T 3 0.07 SIDE CHAIN REMARK 500 DG T 4 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1004 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 116 OE1 REMARK 620 2 GLU A 116 OE2 42.7 REMARK 620 3 HOH A1058 O 63.4 56.9 REMARK 620 4 HOH A1086 O 76.9 96.1 140.2 REMARK 620 5 HOH A1173 O 104.8 66.5 101.5 91.3 REMARK 620 6 HOH A1224 O 133.7 135.7 82.0 127.8 111.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 411 OD1 REMARK 620 2 ASP A 411 OD2 49.0 REMARK 620 3 LEU A 412 O 57.6 91.3 REMARK 620 4 ASP A 623 OD1 117.0 78.4 99.3 REMARK 620 5 TTP A1005 O2A 132.7 91.3 165.1 66.9 REMARK 620 6 TTP A1005 O2B 158.7 148.2 102.7 71.2 68.3 REMARK 620 7 TTP A1005 O1G 90.0 115.5 106.2 150.2 85.8 88.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 411 OD2 REMARK 620 2 ASP A 623 OD2 64.8 REMARK 620 3 SER A 624 OG 52.8 62.0 REMARK 620 4 TTP A1005 O2A 82.1 68.0 122.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 686 OE1 REMARK 620 2 HOH A1176 O 93.9 REMARK 620 3 HOH A1278 O 146.1 60.4 REMARK 620 4 HOH A1283 O 159.1 98.7 54.3 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 CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WAJ RELATED DB: PDB REMARK 900 PREVIOUSLY-DETERMINED APO STRUCTURE OF THIS POLYMERASE REMARK 900 RELATED ID: 1CLQ RELATED DB: PDB REMARK 900 PREVIOUSLY-DETERMINED STRUCTURE OF THIS POLYMERASE IN ITS EDITING REMARK 900 MODE DBREF 1IG9 A 1 903 UNP Q38087 DPOL_BPR69 1 903 DBREF 1IG9 T 1 18 PDB 1IG9 1IG9 1 18 DBREF 1IG9 P 102 115 PDB 1IG9 1IG9 102 115 SEQADV 1IG9 ALA A 222 UNP Q38087 ASP 222 ENGINEERED MUTATION SEQADV 1IG9 ALA A 327 UNP Q38087 ASP 327 ENGINEERED MUTATION SEQRES 1 T 18 DA DC DA DG DG DT DA DA DG DC DA DG DT SEQRES 2 T 18 DC DC DG DC DG SEQRES 1 P 14 DG DC DG DG DA DC DT DG DC DT DT DA DC SEQRES 2 P 14 DOC SEQRES 1 A 903 MET LYS GLU PHE TYR LEU THR VAL GLU GLN ILE GLY ASP SEQRES 2 A 903 SER ILE PHE GLU ARG TYR ILE ASP SER ASN GLY ARG GLU SEQRES 3 A 903 ARG THR ARG GLU VAL GLU TYR LYS PRO SER LEU PHE ALA SEQRES 4 A 903 HIS CYS PRO GLU SER GLN ALA THR LYS TYR PHE ASP ILE SEQRES 5 A 903 TYR GLY LYS PRO CYS THR ARG LYS LEU PHE ALA ASN MET SEQRES 6 A 903 ARG ASP ALA SER GLN TRP ILE LYS ARG MET GLU ASP ILE SEQRES 7 A 903 GLY LEU GLU ALA LEU GLY MET ASP ASP PHE LYS LEU ALA SEQRES 8 A 903 TYR LEU SER ASP THR TYR ASN TYR GLU ILE LYS TYR ASP SEQRES 9 A 903 HIS THR LYS ILE ARG VAL ALA ASN PHE ASP ILE GLU VAL SEQRES 10 A 903 THR SER PRO ASP GLY PHE PRO GLU PRO SER GLN ALA LYS SEQRES 11 A 903 HIS PRO ILE ASP ALA ILE THR HIS TYR ASP SER ILE ASP SEQRES 12 A 903 ASP ARG PHE TYR VAL PHE ASP LEU LEU ASN SER PRO TYR SEQRES 13 A 903 GLY ASN VAL GLU GLU TRP SER ILE GLU ILE ALA ALA LYS SEQRES 14 A 903 LEU GLN GLU GLN GLY GLY ASP GLU VAL PRO SER GLU ILE SEQRES 15 A 903 ILE ASP LYS ILE ILE TYR MET PRO PHE ASP ASN GLU LYS SEQRES 16 A 903 GLU LEU LEU MET GLU TYR LEU ASN PHE TRP GLN GLN LYS SEQRES 17 A 903 THR PRO VAL ILE LEU THR GLY TRP ASN VAL GLU SER PHE SEQRES 18 A 903 ALA ILE PRO TYR VAL TYR ASN ARG ILE LYS ASN ILE PHE SEQRES 19 A 903 GLY GLU SER THR ALA LYS ARG LEU SER PRO HIS ARG LYS SEQRES 20 A 903 THR ARG VAL LYS VAL ILE GLU ASN MET TYR GLY SER ARG SEQRES 21 A 903 GLU ILE ILE THR LEU PHE GLY ILE SER VAL LEU ASP TYR SEQRES 22 A 903 ILE ASP LEU TYR LYS LYS PHE SER PHE THR ASN GLN PRO SEQRES 23 A 903 SER TYR SER LEU ASP TYR ILE SER GLU PHE GLU LEU ASN SEQRES 24 A 903 VAL GLY LYS LEU LYS TYR ASP GLY PRO ILE SER LYS LEU SEQRES 25 A 903 ARG GLU SER ASN HIS GLN ARG TYR ILE SER TYR ASN ILE SEQRES 26 A 903 ILE ALA VAL TYR ARG VAL LEU GLN ILE ASP ALA LYS ARG SEQRES 27 A 903 GLN PHE ILE ASN LEU SER LEU ASP MET GLY TYR TYR ALA SEQRES 28 A 903 LYS ILE GLN ILE GLN SER VAL PHE SER PRO ILE LYS THR SEQRES 29 A 903 TRP ASP ALA ILE ILE PHE ASN SER LEU LYS GLU GLN ASN SEQRES 30 A 903 LYS VAL ILE PRO GLN GLY ARG SER HIS PRO VAL GLN PRO SEQRES 31 A 903 TYR PRO GLY ALA PHE VAL LYS GLU PRO ILE PRO ASN ARG SEQRES 32 A 903 TYR LYS TYR VAL MET SER PHE ASP LEU THR SER LEU TYR SEQRES 33 A 903 PRO SER ILE ILE ARG GLN VAL ASN ILE SER PRO GLU THR SEQRES 34 A 903 ILE ALA GLY THR PHE LYS VAL ALA PRO LEU HIS ASP TYR SEQRES 35 A 903 ILE ASN ALA VAL ALA GLU ARG PRO SER ASP VAL TYR SER SEQRES 36 A 903 CYS SER PRO ASN GLY MET MET TYR TYR LYS ASP ARG ASP SEQRES 37 A 903 GLY VAL VAL PRO THR GLU ILE THR LYS VAL PHE ASN GLN SEQRES 38 A 903 ARG LYS GLU HIS LYS GLY TYR MET LEU ALA ALA GLN ARG SEQRES 39 A 903 ASN GLY GLU ILE ILE LYS GLU ALA LEU HIS ASN PRO ASN SEQRES 40 A 903 LEU SER VAL ASP GLU PRO LEU ASP VAL ASP TYR ARG PHE SEQRES 41 A 903 ASP PHE SER ASP GLU ILE LYS GLU LYS ILE LYS LYS LEU SEQRES 42 A 903 SER ALA LYS SER LEU ASN GLU MET LEU PHE ARG ALA GLN SEQRES 43 A 903 ARG THR GLU VAL ALA GLY MET THR ALA GLN ILE ASN ARG SEQRES 44 A 903 LYS LEU LEU ILE ASN SER LEU TYR GLY ALA LEU GLY ASN SEQRES 45 A 903 VAL TRP PHE ARG TYR TYR ASP LEU ARG ASN ALA THR ALA SEQRES 46 A 903 ILE THR THR PHE GLY GLN MET ALA LEU GLN TRP ILE GLU SEQRES 47 A 903 ARG LYS VAL ASN GLU TYR LEU ASN GLU VAL CYS GLY THR SEQRES 48 A 903 GLU GLY GLU ALA PHE VAL LEU TYR GLY ASP THR ASP SER SEQRES 49 A 903 ILE TYR VAL SER ALA ASP LYS ILE ILE ASP LYS VAL GLY SEQRES 50 A 903 GLU SER LYS PHE ARG ASP THR ASN HIS TRP VAL ASP PHE SEQRES 51 A 903 LEU ASP LYS PHE ALA ARG GLU ARG MET GLU PRO ALA ILE SEQRES 52 A 903 ASP ARG GLY PHE ARG GLU MET CYS GLU TYR MET ASN ASN SEQRES 53 A 903 LYS GLN HIS LEU MET PHE MET ASP ARG GLU ALA ILE ALA SEQRES 54 A 903 GLY PRO PRO LEU GLY SER LYS GLY ILE GLY GLY PHE TRP SEQRES 55 A 903 THR GLY LYS LYS ARG TYR ALA LEU ASN VAL TRP ASP MET SEQRES 56 A 903 GLU GLY THR ARG TYR ALA GLU PRO LYS LEU LYS ILE MET SEQRES 57 A 903 GLY LEU GLU THR GLN LYS SER SER THR PRO LYS ALA VAL SEQRES 58 A 903 GLN LYS ALA LEU LYS GLU CYS ILE ARG ARG MET LEU GLN SEQRES 59 A 903 GLU GLY GLU GLU SER LEU GLN GLU TYR PHE LYS GLU PHE SEQRES 60 A 903 GLU LYS GLU PHE ARG GLN LEU ASN TYR ILE SER ILE ALA SEQRES 61 A 903 SER VAL SER SER ALA ASN ASN ILE ALA LYS TYR ASP VAL SEQRES 62 A 903 GLY GLY PHE PRO GLY PRO LYS CYS PRO PHE HIS ILE ARG SEQRES 63 A 903 GLY ILE LEU THR TYR ASN ARG ALA ILE LYS GLY ASN ILE SEQRES 64 A 903 ASP ALA PRO GLN VAL VAL GLU GLY GLU LYS VAL TYR VAL SEQRES 65 A 903 LEU PRO LEU ARG GLU GLY ASN PRO PHE GLY ASP LYS CYS SEQRES 66 A 903 ILE ALA TRP PRO SER GLY THR GLU ILE THR ASP LEU ILE SEQRES 67 A 903 LYS ASP ASP VAL LEU HIS TRP MET ASP TYR THR VAL LEU SEQRES 68 A 903 LEU GLU LYS THR PHE ILE LYS PRO LEU GLU GLY PHE THR SEQRES 69 A 903 SER ALA ALA LYS LEU ASP TYR GLU LYS LYS ALA SER LEU SEQRES 70 A 903 PHE ASP MET PHE ASP PHE MODRES 1IG9 DOC P 115 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC P 115 18 HET CA A1001 1 HET CA A1002 1 HET CA A1003 1 HET CA A1004 1 HET TTP A1005 29 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 CA 4(CA 2+) FORMUL 8 TTP C10 H17 N2 O14 P3 FORMUL 9 HOH *356(H2 O) HELIX 1 1 ASN A 64 ASP A 77 1 14 HELIX 2 2 ASP A 87 TYR A 97 1 11 HELIX 3 3 ASP A 104 ILE A 108 5 5 HELIX 4 4 SER A 163 LYS A 169 1 7 HELIX 5 5 LEU A 170 GLY A 174 5 5 HELIX 6 6 PRO A 179 ASP A 184 1 6 HELIX 7 7 ASN A 193 LYS A 208 1 16 HELIX 8 8 PHE A 221 GLY A 235 1 15 HELIX 9 9 GLY A 235 LYS A 240 1 6 HELIX 10 10 ARG A 241 SER A 243 5 3 HELIX 11 11 ASP A 272 SER A 281 1 10 HELIX 12 12 SER A 289 ASN A 299 1 11 HELIX 13 13 PRO A 308 ASN A 316 1 9 HELIX 14 14 ASN A 316 GLN A 339 1 24 HELIX 15 15 GLN A 339 LYS A 352 1 14 HELIX 16 16 GLN A 354 PHE A 359 5 6 HELIX 17 17 SER A 360 GLN A 376 1 17 HELIX 18 18 SER A 414 ASN A 424 1 11 HELIX 19 19 PRO A 438 ASN A 444 1 7 HELIX 20 20 GLY A 469 LEU A 503 1 35 HELIX 21 21 SER A 523 LYS A 531 1 9 HELIX 22 22 SER A 534 GLY A 571 1 38 HELIX 23 23 ASP A 579 GLY A 610 1 32 HELIX 24 24 ALA A 629 LYS A 635 1 7 HELIX 25 25 ASP A 643 ARG A 658 1 16 HELIX 26 26 ARG A 658 MET A 674 1 17 HELIX 27 27 LEU A 730 LYS A 734 5 5 HELIX 28 28 PRO A 738 GLU A 755 1 18 HELIX 29 29 GLY A 756 PHE A 771 1 16 HELIX 30 30 ARG A 772 LEU A 774 5 3 HELIX 31 31 ASN A 775 ALA A 780 5 6 HELIX 32 32 ILE A 788 ASP A 792 5 5 HELIX 33 33 PRO A 802 ILE A 815 1 14 HELIX 34 34 THR A 855 TRP A 865 1 11 HELIX 35 35 ASP A 867 PHE A 876 1 10 HELIX 36 36 PHE A 876 ALA A 887 1 12 SHEET 1 A 3 PHE A 4 ILE A 11 0 SHEET 2 A 3 SER A 14 ILE A 20 -1 O SER A 14 N ILE A 11 SHEET 3 A 3 GLU A 26 VAL A 31 -1 N ARG A 27 O TYR A 19 SHEET 1 B 2 SER A 36 HIS A 40 0 SHEET 2 B 2 CYS A 57 LEU A 61 -1 N THR A 58 O ALA A 39 SHEET 1 C 2 PHE A 50 ASP A 51 0 SHEET 2 C 2 LYS A 378 VAL A 379 1 N VAL A 379 O PHE A 50 SHEET 1 D 6 ILE A 186 PHE A 191 0 SHEET 2 D 6 ARG A 145 LEU A 151 1 O PHE A 146 N ILE A 187 SHEET 3 D 6 ILE A 133 ASP A 140 -1 O ASP A 134 N LEU A 151 SHEET 4 D 6 VAL A 110 VAL A 117 -1 O ASN A 112 N TYR A 139 SHEET 5 D 6 ILE A 212 THR A 214 1 O ILE A 212 N ALA A 111 SHEET 6 D 6 SER A 269 VAL A 270 1 O SER A 269 N LEU A 213 SHEET 1 E 2 THR A 248 LYS A 251 0 SHEET 2 E 2 ILE A 262 LEU A 265 -1 N ILE A 262 O LYS A 251 SHEET 1 F 2 GLU A 254 ASN A 255 0 SHEET 2 F 2 GLY A 258 SER A 259 -1 O GLY A 258 N ASN A 255 SHEET 1 G 6 THR A 718 MET A 728 0 SHEET 2 G 6 ARG A 707 MET A 715 -1 O TYR A 708 N MET A 728 SHEET 3 G 6 MET A 683 ALA A 689 -1 O ILE A 688 N TRP A 713 SHEET 4 G 6 VAL A 407 LEU A 412 -1 O VAL A 407 N ALA A 689 SHEET 5 G 6 SER A 624 SER A 628 -1 O ILE A 625 N PHE A 410 SHEET 6 G 6 VAL A 617 GLY A 620 -1 N LEU A 618 O TYR A 626 SHEET 1 H 4 THR A 718 MET A 728 0 SHEET 2 H 4 ARG A 707 MET A 715 -1 O TYR A 708 N MET A 728 SHEET 3 H 4 GLY A 700 GLY A 704 -1 O PHE A 701 N ALA A 709 SHEET 4 H 4 ASN A 402 ARG A 403 -1 O ASN A 402 N TRP A 702 SHEET 1 I 3 ILE A 430 THR A 433 0 SHEET 2 I 3 MET A 461 TYR A 463 -1 O MET A 462 N ALA A 431 SHEET 3 I 3 SER A 455 SER A 457 -1 N SER A 455 O TYR A 463 SHEET 1 J 3 SER A 781 SER A 784 0 SHEET 2 J 3 LYS A 829 PRO A 834 -1 N VAL A 830 O SER A 783 SHEET 3 J 3 CYS A 845 PRO A 849 -1 N ILE A 846 O LEU A 833 LINK O3' DC P 114 P DOC P 115 1555 1555 1.61 LINK OE1 GLU A 116 CA CA A1004 1555 1555 2.99 LINK OE2 GLU A 116 CA CA A1004 1555 1555 3.05 LINK OD1 ASP A 411 CA CA A1001 1555 1555 2.68 LINK OD2 ASP A 411 CA CA A1001 1555 1555 2.64 LINK OD2 ASP A 411 CA CA A1002 1555 1555 2.97 LINK O LEU A 412 CA CA A1001 1555 1555 2.62 LINK OD1 ASP A 623 CA CA A1001 1555 1555 2.59 LINK OD2 ASP A 623 CA CA A1002 1555 1555 3.35 LINK OG SER A 624 CA CA A1002 1555 1555 3.04 LINK OE1 GLU A 686 CA CA A1003 1555 1555 3.25 LINK CA CA A1001 O2A TTP A1005 1555 1555 2.79 LINK CA CA A1001 O2B TTP A1005 1555 1555 2.69 LINK CA CA A1001 O1G TTP A1005 1555 1555 2.63 LINK CA CA A1002 O2A TTP A1005 1555 1555 2.95 LINK CA CA A1003 O HOH A1176 1555 1555 2.79 LINK CA CA A1003 O HOH A1278 1555 1555 3.22 LINK CA CA A1003 O HOH A1283 1555 1555 3.05 LINK CA CA A1004 O HOH A1058 1555 1555 3.14 LINK CA CA A1004 O HOH A1086 1555 1555 3.22 LINK CA CA A1004 O HOH A1173 1555 1555 2.98 LINK CA CA A1004 O HOH A1224 1555 1555 2.89 SITE 1 AC1 4 ASP A 411 LEU A 412 ASP A 623 TTP A1005 SITE 1 AC2 4 ASP A 411 ASP A 623 SER A 624 TTP A1005 SITE 1 AC3 5 ASP A 684 GLU A 686 GLU A 716 HOH A1176 SITE 2 AC3 5 HOH A1283 SITE 1 AC4 3 GLU A 116 HOH A1173 HOH A1224 SITE 1 AC5 17 SER A 414 LEU A 415 TYR A 416 PRO A 417 SITE 2 AC5 17 ARG A 482 LYS A 560 ASN A 564 ASP A 623 SITE 3 AC5 17 CA A1001 CA A1002 HOH A1007 HOH A1176 SITE 4 AC5 17 HOH A1196 HOH A1278 DOC P 115 DA T 3 SITE 5 AC5 17 DG T 4 CRYST1 80.787 118.602 127.997 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 0.012378 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007813 0.00000