HEADER HYDROLASE 19-FEB-03 1ODG TITLE VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO ITS TITLE 2 REACTION PRODUCT 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 COMPND 5 ENDONUCLEASE, 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 KEYWDS 2 REPAIR, DNA 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 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, JRNL AUTH 2 L.H.PEARL JRNL TITL CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI DCM JRNL TITL 2 VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO JRNL TITL 3 ITS 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. 2.8 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) : 2.8 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.7 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 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) : 0.2873 REMARK 3 FREE R VALUE : 0.3561 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.0 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 : 458 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 105 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.190 REMARK 3 B22 (A**2) : -15.190 REMARK 3 B33 (A**2) : 30.380 REMARK 3 B12 (A**2) : -6.172 REMARK 3 B13 (A**2) : 0.0 REMARK 3 B23 (A**2) : 0.0 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) : 0.008265 REMARK 3 BOND ANGLES (DEGREES) : 1.30641 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 ; 1.5 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.381 ; 2.0 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.325 ; 2.0 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.963 ; 2.5 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.318 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. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-03. REMARK 100 THE PDBE ID CODE IS EBI-12201. 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (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 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 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, REMARK 280 15% PEG 8000, 50 MM SODIUM CACODYLATE PH 6.5, REMARK 280 75 MM AMMONIUM SULPHATE AND 10% GLYCEROL PROTEIN 2.5 MG/ML 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 300 DETAILS: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 GENERATING THE BIOMOLECULE 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 OP3 DT F 1 P -0.085 REMARK 500 DT W 1 OP3 DT W 1 P -0.091 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DT F 7 O3' - P - O5' ANGL. DEV. = -17.0 DEGREES REMARK 500 DT F 7 O3' - P - OP1 ANGL. DEV. = 40.7 DEGREES REMARK 500 DT F 7 O3' - P - OP2 ANGL. DEV. = 40.7 DEGREES REMARK 500 DT F 7 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 DT W 7 O3' - P - O5' ANGL. DEV. = 22.9 DEGREES REMARK 500 DT W 7 O3' - P - OP1 ANGL. DEV. = 10.0 DEGREES REMARK 500 DT W 7 O3' - P - OP2 ANGL. DEV. = 10.0 DEGREES 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 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 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 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 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 REMARK 900 PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX REMARK 900 WITH A DUPLEX DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1VSR RELATED DB: PDB REMARK 900 VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE REMARK 900 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 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 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 MODRES 1ODG 5CM F 6 C 5-METHYL-2'-DEOXY-5'-CYTIDINE-5'-MONOPHOSPHATE MODRES 1ODG 5CM W 6 C 5-METHYL-2'-DEOXY-5'-CYTIDINE-5'-MONOPHOSPHATE 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 1 5CM 2() FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *81(H2 O1) 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 ZN ZN A 200 SG CYS A 66 1555 1555 2.15 LINK ZN ZN A 200 SG CYS A 117 1555 1555 2.51 LINK ZN ZN A 200 SG CYS A 73 1555 1555 1.95 LINK ZN ZN A 200 ND1 HIS A 71 1555 1555 1.86 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 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