PDB Short entry for 1ODG HEADER HYDROLASE 19-FEB-03 1ODG TITLE VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO ITS REACTION PRODUCT TITLE 2 SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA MISMATCH ENDONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VERY SHORT PATCH REPAIR PROTEIN, VSR MISMATCH ENDONUCLEASE, COMPND 5 V.ECOKDCM, VSR, B1960; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'; COMPND 9 CHAIN: F, W SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834 (DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS HYDROLASE, DNA REPAIR, ENDONUCLEASE, VERY SHORT PATCH REPAIR, DNA KEYWDS 2 REPAI HYDROLASE, NUCLEASE, ZINC, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.A.BUNTING,S.M.ROE,A.HEADLEY,T.BROWN,R.SAVVA,L.H.PEARL REVDAT 3 13-DEC-23 1ODG 1 REMARK LINK REVDAT 2 24-FEB-09 1ODG 1 VERSN REVDAT 1 13-MAR-03 1ODG 0 JRNL AUTH K.A.BUNTING,S.M.ROE,A.HEADLEY,T.BROWN,R.SAVVA,L.H.PEARL JRNL TITL CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI DCM JRNL TITL 2 VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO ITS JRNL TITL 3 REACTION PRODUCT-SITE IN A DNA SUPERHELIX JRNL REF NUCLEIC ACIDS RES. V. 31 1633 2003 JRNL REFN ISSN 0305-1048 JRNL PMID 12626704 JRNL DOI 10.1093/NAR/GKG273 REMARK 2 REMARK 2 RESOLUTION. 2.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.70 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) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 9535 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) : 0.287 REMARK 3 FREE R VALUE : 0.356 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 923 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1092 REMARK 3 NUCLEIC ACID ATOMS : 498 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 105.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.19000 REMARK 3 B22 (A**2) : -15.19000 REMARK 3 B33 (A**2) : 30.38000 REMARK 3 B12 (A**2) : -6.17200 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.306 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 1.372 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.381 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.325 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.963 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 74.25 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 : LHP_DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : LHP_DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ODG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1290012201. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10084 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1CW0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM HEPES PH7.0, 75 MM NACL, 15% PEG REMARK 280 8000, 50 MM SODIUM CACODYLATE PH 6.5, 75 MM AMMONIUM SULPHATE REMARK 280 AND 10% GLYCEROL PROTEIN 2.5 MG/ML, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.43000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.86000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.14500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.57500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 10.71500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE TRIMERIC ASSEMBLY DESCRIBED HERE IS REMARK 300 FORMED BYTHE COMPLEX OF PROTEIN CHAIN A WITH DNA REMARK 300 CHAINS F,W REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, W 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 FUNCTIONS IN THE DEAMINATION OF 5-METHYLCYTOSINE IN REMARK 400 DNA CAUSING MISMATCHES IN T/G WHICH CAN LEAD TO C-TO-T REMARK 400 TRANSITION MUTATIONS IF UNREPAIRED. 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 77 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2014 O HOH F 2017 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT F 1 P DT F 1 OP3 -0.085 REMARK 500 DT W 1 P DT W 1 OP3 -0.091 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 24 -22.59 -152.07 REMARK 500 ARG A 27 -39.33 -31.57 REMARK 500 LEU A 37 117.32 -4.33 REMARK 500 GLN A 42 85.71 20.72 REMARK 500 PRO A 47 155.89 -49.51 REMARK 500 ARG A 49 78.26 26.45 REMARK 500 PRO A 50 169.74 -47.20 REMARK 500 TYR A 57 0.13 -155.85 REMARK 500 THR A 63 75.98 -117.93 REMARK 500 HIS A 70 66.50 39.24 REMARK 500 CYS A 117 -18.66 -46.86 REMARK 500 LEU A 119 -0.61 -148.53 REMARK 500 ARG A 122 47.95 -76.05 REMARK 500 GLU A 123 -3.81 -173.87 REMARK 500 ASP A 127 -15.26 -44.81 REMARK 500 ALA A 129 -35.64 -34.05 REMARK 500 LEU A 130 -70.74 -63.90 REMARK 500 TRP A 137 -99.98 -92.86 REMARK 500 ILE A 138 -63.26 -7.46 REMARK 500 GLU A 141 174.26 47.60 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 DG F 8 0.07 SIDE CHAIN REMARK 500 DG F 9 0.05 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 ZN A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 HIS A 71 ND1 113.7 REMARK 620 3 CYS A 73 SG 99.1 124.2 REMARK 620 4 CYS A 117 SG 104.2 100.1 114.5 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 ZN A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CW0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) REMARK 900 ENDONUCLEASE IN COMPLEX WITH A DUPLEX DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1VSR RELATED DB: PDB REMARK 900 VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI DBREF 1ODG A 23 156 UNP P09184 VSR_ECOLI 22 155 DBREF 1ODG F 1 12 PDB 1ODG 1ODG 1 12 DBREF 1ODG W 1 12 PDB 1ODG 1ODG 1 12 SEQRES 1 A 134 ALA ILE GLU LYS ARG LEU ALA SER LEU LEU THR GLY GLN SEQRES 2 A 134 GLY LEU ALA PHE ARG VAL GLN ASP ALA SER LEU PRO GLY SEQRES 3 A 134 ARG PRO ASP PHE VAL VAL ASP GLU TYR ARG CYS VAL ILE SEQRES 4 A 134 PHE THR HIS GLY CYS PHE TRP HIS HIS HIS HIS CYS TYR SEQRES 5 A 134 LEU PHE LYS VAL PRO ALA THR ARG THR GLU PHE TRP LEU SEQRES 6 A 134 GLU LYS ILE GLY LYS ASN VAL GLU ARG ASP ARG ARG ASP SEQRES 7 A 134 ILE SER ARG LEU GLN GLU LEU GLY TRP ARG VAL LEU ILE SEQRES 8 A 134 VAL TRP GLU CYS ALA LEU ARG GLY ARG GLU LYS LEU THR SEQRES 9 A 134 ASP GLU ALA LEU THR GLU ARG LEU GLU GLU TRP ILE CYS SEQRES 10 A 134 GLY GLU GLY ALA SER ALA GLN ILE ASP THR GLN GLY ILE SEQRES 11 A 134 HIS LEU LEU ALA SEQRES 1 F 12 DT DA DG DG DC 5CM DT DG DG DA DT DC SEQRES 1 W 12 DT DA DG DG DC 5CM DT DG DG DA DT DC MODRES 1ODG 5CM F 6 DC MODRES 1ODG 5CM W 6 DC HET 5CM F 6 20 HET 5CM W 6 20 HET ZN A 200 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *81(H2 O) HELIX 1 1 ILE A 24 THR A 33 1 10 HELIX 2 2 GLY A 34 GLY A 36 5 3 HELIX 3 3 ARG A 82 LEU A 107 1 26 HELIX 4 4 GLU A 116 LEU A 119 5 4 HELIX 5 5 THR A 126 CYS A 139 1 14 SHEET 1 AA 6 PHE A 39 VAL A 41 0 SHEET 2 AA 6 PHE A 52 VAL A 54 -1 O VAL A 53 N ARG A 40 SHEET 3 AA 6 CYS A 59 PHE A 62 -1 O CYS A 59 N VAL A 54 SHEET 4 AA 6 ARG A 110 VAL A 114 1 O ARG A 110 N VAL A 60 SHEET 5 AA 6 ALA A 145 ASP A 148 1 O ALA A 145 N ILE A 113 SHEET 6 AA 6 GLY A 151 LEU A 154 -1 O GLY A 151 N ASP A 148 LINK O3' DC F 5 P 5CM F 6 1555 1555 1.61 LINK O3' 5CM F 6 P DT F 7 1555 1555 1.62 LINK O3' DC W 5 P 5CM W 6 1555 1555 1.61 LINK O3' 5CM W 6 P DT W 7 1555 1555 1.62 LINK SG CYS A 66 ZN ZN A 200 1555 1555 2.15 LINK ND1 HIS A 71 ZN ZN A 200 1555 1555 1.86 LINK SG CYS A 73 ZN ZN A 200 1555 1555 1.95 LINK SG CYS A 117 ZN ZN A 200 1555 1555 2.51 SITE 1 AC1 4 CYS A 66 HIS A 71 CYS A 73 CYS A 117 CRYST1 102.805 102.805 64.290 90.00 90.00 120.00 P 61 12 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 0.009727 0.005616 0.000000 0.00000 SCALE2 0.000000 0.011232 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015554 0.00000