HEADER TRANSFERASE/DNA 28-JUN-06 2HHW TITLE DDTTP:O6-METHYL-GUANINE PAIR IN THE POLYMERASE ACTIVE SITE, IN THE TITLE 2 CLOSED CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'; COMPND 3 CHAIN: E, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DNA PRIMER STRAND; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'; COMPND 8 CHAIN: F, C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: DNA TEMPLATE STRAND; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA POLYMERASE I; COMPND 13 CHAIN: A, D; COMPND 14 FRAGMENT: RESIDUES 299-876 (ANALOGOUS TO E COLI KLENOW FRAGMENT); 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 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 9 ORGANISM_TAXID: 1422; SOURCE 10 GENE: POLA; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PUC KEYWDS DNA POLYMERASE I, DNA REPLICATION, KLENOW FRAGMENT, DNA-PROTEIN KEYWDS 2 COMPLEX, O6-METHYL-GUANINE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.J.WARREN,L.J.FORSBERG,L.S.BEESE REVDAT 7 30-AUG-23 2HHW 1 HETSYN REVDAT 6 29-JUL-20 2HHW 1 COMPND REMARK HET HETNAM REVDAT 6 2 1 FORMUL LINK SITE ATOM REVDAT 5 13-MAY-20 2HHW 1 HET HETNAM FORMUL LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 18-OCT-17 2HHW 1 REMARK REVDAT 3 24-FEB-09 2HHW 1 VERSN REVDAT 2 16-JAN-07 2HHW 1 JRNL REVDAT 1 12-DEC-06 2HHW 0 JRNL AUTH J.J.WARREN,L.J.FORSBERG,L.S.BEESE JRNL TITL THE STRUCTURAL BASIS FOR THE MUTAGENICITY OF JRNL TITL 2 O6-METHYL-GUANINE LESIONS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 19701 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17179038 JRNL DOI 10.1073/PNAS.0609580103 REMARK 2 REMARK 2 RESOLUTION. 1.88 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 113550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 5689 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.17 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE : 0.2863 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 510 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9304 REMARK 3 NUCLEIC ACID ATOMS : 810 REMARK 3 HETEROGEN ATOMS : 119 REMARK 3 SOLVENT ATOMS : 794 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75800 REMARK 3 B22 (A**2) : -2.21600 REMARK 3 B33 (A**2) : 1.45800 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) : 0.21 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.15 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.150 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 45.06 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:DNA-RNA-MULTI-ENDO-NEW2.PARAM REMARK 3 PARAMETER FILE 4 : D3T.PARAM REMARK 3 PARAMETER FILE 5 : CNS_TOPPAR:SUCROSE.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HHW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-04 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 : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.008 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120016 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.78200 REMARK 200 FOR SHELL : 2.000 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 1LV5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% SATURATED AMMONIUM SULFATE, 2.5% REMARK 280 MPD, 100MM MES, PH 5.8, 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 46.91700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.05550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.44850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.05550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.91700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.44850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 ASYMMETRIC UNIT CONTAINS TWO BIOLOGICAL ASSEMBLIES, REMARK 300 EACH CONSISTING OF ONE PROTEIN MOLECULE, TWO STRANDS OF DNA, AND AN REMARK 300 INCOMING DIDEOXY THYMIDINE TRIPHOSPHATE. CHAINS A, B, C, AND G REMARK 300 CONSTITUTE ONE ASSEMBLY, AND CHAINS D, E, F, AND G CONSTITUTE THE REMARK 300 SECOND. 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, G 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, D, H 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 DC F 0 REMARK 465 DA F 1 REMARK 465 DC C 0 REMARK 465 DA C 1 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 DT F 2 P OP1 OP2 REMARK 470 DT C 2 P OP1 OP2 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 -137.91 -108.90 REMARK 500 LEU A 303 77.94 -100.06 REMARK 500 ASP A 372 65.22 61.89 REMARK 500 ASP A 402 97.09 -171.49 REMARK 500 ALA A 421 35.89 -68.68 REMARK 500 LEU A 477 -74.36 -119.76 REMARK 500 ILE A 588 -71.85 -118.44 REMARK 500 LEU A 610 -56.43 -127.13 REMARK 500 GLU A 620 70.15 35.46 REMARK 500 ILE A 628 -26.54 -162.87 REMARK 500 GLN A 656 43.02 34.12 REMARK 500 ARG A 819 20.74 49.96 REMARK 500 HIS A 829 -53.63 72.33 REMARK 500 LEU D 312 42.41 -106.88 REMARK 500 ASP D 372 62.78 61.89 REMARK 500 ASP D 402 95.11 -166.20 REMARK 500 ALA D 421 39.99 -84.74 REMARK 500 ILE D 588 -72.55 -116.51 REMARK 500 LEU D 610 -54.86 -130.66 REMARK 500 GLU D 620 69.37 36.91 REMARK 500 ILE D 628 -24.99 -164.62 REMARK 500 GLN D 656 48.53 35.39 REMARK 500 HIS D 829 -50.69 70.62 REMARK 500 ASP D 830 19.04 -141.88 REMARK 500 ALA D 875 41.38 -86.24 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 MN A 878 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 653 OD1 REMARK 620 2 TYR A 654 O 80.1 REMARK 620 3 ASP A 830 OD2 89.6 91.9 REMARK 620 4 D3T A 881 O1A 114.6 165.3 88.0 REMARK 620 5 D3T A 881 O1G 96.9 88.6 173.5 89.8 REMARK 620 6 D3T A 881 O2B 170.2 90.2 91.9 75.1 81.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 878 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 653 OD1 REMARK 620 2 TYR D 654 O 81.0 REMARK 620 3 ASP D 830 OD2 87.1 90.8 REMARK 620 4 D3T D 880 O2G 94.4 89.1 178.5 REMARK 620 5 D3T D 880 O2A 110.9 167.9 87.6 92.1 REMARK 620 6 D3T D 880 O1B 166.7 87.6 100.1 78.4 80.8 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HHQ RELATED DB: PDB REMARK 900 RELATED ID: 2HHS RELATED DB: PDB REMARK 900 RELATED ID: 2HHT RELATED DB: PDB REMARK 900 RELATED ID: 2HHU RELATED DB: PDB REMARK 900 RELATED ID: 2HHV RELATED DB: PDB REMARK 900 RELATED ID: 2HHX RELATED DB: PDB REMARK 900 RELATED ID: 2HHY RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT UNP REMARK 999 SEQUENCE DATABASE AT THE TIME OF PROCESSING. THE SEQUENCE REMARK 999 OF THIS PROTEIN IS ANALOGOUS TO GEOBACILLUS KAUSTOPHILUS, REMARK 999 UNP ACCESSION, Q5KWC1_GEOKA. DBREF 2HHW A 297 876 UNP Q5KWC1 Q5KWC1_GEOKA 299 878 DBREF 2HHW D 297 876 UNP Q5KWC1 Q5KWC1_GEOKA 299 878 DBREF 2HHW E 21 29 PDB 2HHW 2HHW 21 29 DBREF 2HHW F 0 12 PDB 2HHW 2HHW 0 12 DBREF 2HHW B 21 29 PDB 2HHW 2HHW 21 29 DBREF 2HHW C 0 12 PDB 2HHW 2HHW 0 12 SEQRES 1 E 9 DC DC DT DG DA DC DT DC DDG SEQRES 1 F 13 DC DA DT 6OG DC DG DA DG DT DC DA DG DG SEQRES 1 B 9 DC DC DT DG DA DC DT DC DDG SEQRES 1 C 13 DC DA DT 6OG DC DG DA DG DT DC DA DG DG 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 ALA 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 TYR 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 SEQRES 1 D 580 ALA LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU SEQRES 2 D 580 GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL SEQRES 3 D 580 VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE SEQRES 4 D 580 ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO SEQRES 5 D 580 GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU SEQRES 6 D 580 GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS SEQRES 7 D 580 ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU SEQRES 8 D 580 CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU SEQRES 9 D 580 LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA SEQRES 10 D 580 ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU SEQRES 11 D 580 ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP SEQRES 12 D 580 GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA SEQRES 13 D 580 ALA ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU SEQRES 14 D 580 ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU SEQRES 15 D 580 GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA SEQRES 16 D 580 GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY SEQRES 17 D 580 LYS GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG SEQRES 18 D 580 ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER SEQRES 19 D 580 PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN SEQRES 20 D 580 LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SEQRES 21 D 580 SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU SEQRES 22 D 580 ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS SEQRES 23 D 580 LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL SEQRES 24 D 580 ARG PRO ALA THR LYS LYS VAL HIS THR ILE PHE ASN GLN SEQRES 25 D 580 ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO SEQRES 26 D 580 ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG SEQRES 27 D 580 LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP SEQRES 28 D 580 LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG SEQRES 29 D 580 VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU SEQRES 30 D 580 ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA SEQRES 31 D 580 MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO SEQRES 32 D 580 ASN MET ARG ARG GLN ALA LYS ALA VAL ASN TYR GLY ILE SEQRES 33 D 580 VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU SEQRES 34 D 580 ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG SEQRES 35 D 580 TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU SEQRES 36 D 580 ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR SEQRES 37 D 580 THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SEQRES 38 D 580 SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET SEQRES 39 D 580 ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE SEQRES 40 D 580 ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS SEQRES 41 D 580 GLU GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS SEQRES 42 D 580 ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU SEQRES 43 D 580 ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA SEQRES 44 D 580 VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR SEQRES 45 D 580 GLY SER THR TRP TYR ASP ALA LYS MODRES 2HHW DDG E 29 DG MODRES 2HHW 6OG F 3 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE MODRES 2HHW DDG B 29 DG MODRES 2HHW 6OG C 3 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HET DDG E 29 21 HET 6OG F 3 23 HET DDG B 29 21 HET 6OG C 3 23 HET GLC G 1 11 HET FRU G 2 12 HET GLC H 1 11 HET FRU H 2 12 HET MN A 878 1 HET SO4 A 879 5 HET SO4 A 880 5 HET D3T A 881 28 HET MN D 878 1 HET SO4 D 879 5 HET D3T D 880 28 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION HETNAM D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 1 DDG 2(C10 H14 N5 O6 P) FORMUL 2 6OG 2(C11 H16 N5 O7 P) FORMUL 7 GLC 2(C6 H12 O6) FORMUL 7 FRU 2(C6 H12 O6) FORMUL 9 MN 2(MN 2+) FORMUL 10 SO4 3(O4 S 2-) FORMUL 12 D3T 2(C10 H17 N2 O13 P3) FORMUL 16 HOH *794(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 GLY A 362 1 9 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 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 GLU A 569 ILE A 588 1 20 HELIX 17 17 ILE A 588 VAL A 595 1 8 HELIX 18 18 LEU A 630 LYS A 635 1 6 HELIX 19 19 ILE A 636 GLN A 638 5 3 HELIX 20 20 GLN A 656 GLU A 667 1 12 HELIX 21 21 ASP A 668 ARG A 677 1 10 HELIX 22 22 ASP A 680 PHE A 690 1 11 HELIX 23 23 SER A 693 VAL A 697 5 5 HELIX 24 24 THR A 698 TYR A 714 1 17 HELIX 25 25 SER A 717 LEU A 725 1 9 HELIX 26 26 SER A 728 PHE A 743 1 16 HELIX 27 27 PHE A 743 GLY A 761 1 19 HELIX 28 28 PRO A 774 SER A 778 5 5 HELIX 29 29 ASN A 780 GLU A 818 1 39 HELIX 30 30 GLU A 840 GLN A 854 1 15 HELIX 31 31 THR D 308 ALA D 313 5 6 HELIX 32 32 ARG D 347 LEU D 352 1 6 HELIX 33 33 ASP D 354 GLY D 362 1 9 HELIX 34 34 ASP D 372 TRP D 382 1 11 HELIX 35 35 LEU D 394 ASP D 402 1 9 HELIX 36 36 PRO D 403 GLY D 406 5 4 HELIX 37 37 ASP D 409 MET D 416 1 8 HELIX 38 38 PRO D 424 GLY D 430 1 7 HELIX 39 39 LYS D 431 ARG D 435 5 5 HELIX 40 40 ASP D 439 ASN D 468 1 30 HELIX 41 41 GLN D 470 LEU D 477 1 8 HELIX 42 42 LEU D 477 GLY D 492 1 16 HELIX 43 43 ASP D 496 GLY D 523 1 28 HELIX 44 44 SER D 530 GLU D 540 1 11 HELIX 45 45 SER D 557 LEU D 564 1 8 HELIX 46 46 GLU D 569 ILE D 588 1 20 HELIX 47 47 ILE D 588 VAL D 595 1 8 HELIX 48 48 LEU D 630 LYS D 635 1 6 HELIX 49 49 ILE D 636 GLN D 638 5 3 HELIX 50 50 GLN D 656 GLU D 667 1 12 HELIX 51 51 ASP D 668 ARG D 677 1 10 HELIX 52 52 ASP D 680 GLN D 691 1 12 HELIX 53 53 THR D 698 TYR D 714 1 17 HELIX 54 54 SER D 717 LEU D 725 1 9 HELIX 55 55 SER D 728 PHE D 743 1 16 HELIX 56 56 PHE D 743 GLY D 761 1 19 HELIX 57 57 PRO D 774 SER D 778 5 5 HELIX 58 58 ASN D 780 GLU D 818 1 39 HELIX 59 59 GLU D 840 GLN D 854 1 15 HELIX 60 60 THR D 871 ALA D 875 5 5 SHEET 1 A 6 THR A 302 LEU A 303 0 SHEET 2 A 6 GLY A 342 LEU A 346 1 O 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 SHEET 1 F 6 THR D 302 LEU D 303 0 SHEET 2 F 6 GLY D 342 LEU D 346 1 O ARG D 343 N THR D 302 SHEET 3 F 6 GLY D 334 ASN D 339 -1 N VAL D 337 O PHE D 344 SHEET 4 F 6 LYS D 315 GLU D 321 -1 N ALA D 317 O VAL D 338 SHEET 5 F 6 LYS D 367 MET D 370 1 O SER D 369 N LEU D 318 SHEET 6 F 6 VAL D 390 ASP D 393 1 O PHE D 392 N MET D 370 SHEET 1 G 3 LYS D 601 VAL D 602 0 SHEET 2 G 3 VAL D 493 VAL D 495 -1 N VAL D 493 O VAL D 602 SHEET 3 G 3 PHE D 640 VAL D 641 -1 O VAL D 641 N LYS D 494 SHEET 1 H 2 LYS D 549 THR D 550 0 SHEET 2 H 2 GLY D 553 TYR D 554 -1 O GLY D 553 N THR D 550 SHEET 1 I 2 ILE D 605 ASN D 607 0 SHEET 2 I 2 SER D 617 THR D 619 -1 O THR D 619 N ILE D 605 SHEET 1 J 4 HIS D 823 GLN D 827 0 SHEET 2 J 4 GLU D 831 PRO D 837 -1 O ILE D 833 N LEU D 825 SHEET 3 J 4 TRP D 647 TYR D 654 -1 N PHE D 650 O LEU D 834 SHEET 4 J 4 VAL D 864 GLY D 869 -1 O ASP D 865 N ASP D 653 SHEET 1 K 2 TYR D 762 THR D 764 0 SHEET 2 K 2 ARG D 770 TYR D 772 -1 O ARG D 771 N VAL D 763 LINK O3' DC E 28 P DDG E 29 1555 1555 1.61 LINK O3' DT F 2 P 6OG F 3 1555 1555 1.60 LINK O3' 6OG F 3 P DC F 4 1555 1555 1.61 LINK O3' DC B 28 P DDG B 29 1555 1555 1.61 LINK O3' DT C 2 P 6OG C 3 1555 1555 1.61 LINK O3' 6OG C 3 P DC C 4 1555 1555 1.61 LINK C1 GLC G 1 O2 FRU G 2 1555 1555 1.46 LINK C1 GLC H 1 O2 FRU H 2 1555 1555 1.46 LINK OD1 ASP A 653 MN MN A 878 1555 1555 2.10 LINK O TYR A 654 MN MN A 878 1555 1555 2.18 LINK OD2 ASP A 830 MN MN A 878 1555 1555 2.08 LINK MN MN A 878 O1A D3T A 881 1555 1555 2.18 LINK MN MN A 878 O1G D3T A 881 1555 1555 2.03 LINK MN MN A 878 O2B D3T A 881 1555 1555 2.13 LINK OD1 ASP D 653 MN MN D 878 1555 1555 2.19 LINK O TYR D 654 MN MN D 878 1555 1555 2.18 LINK OD2 ASP D 830 MN MN D 878 1555 1555 2.08 LINK MN MN D 878 O2G D3T D 880 1555 1555 2.01 LINK MN MN D 878 O2A D3T D 880 1555 1555 2.17 LINK MN MN D 878 O1B D3T D 880 1555 1555 2.05 CISPEP 1 GLU A 620 PRO A 621 0 -0.13 CISPEP 2 GLU D 620 PRO D 621 0 -0.16 CRYST1 93.834 108.897 150.111 90.00 90.00 90.00 P 21 21 21 8 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 0.010657 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006662 0.00000