HEADER HYDROLASE 06-NOV-08 2W35 TITLE STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF DEAMINATED TITLE 2 ADENINE REPAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE V; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEOXYINOSINE 3'ENDONUCLEASE,DEOXYRIBONUCLEASE V,DNASE V; COMPND 5 EC: 3.1.21.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3'; COMPND 9 CHAIN: C, F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*AP*GP*CP*CP*GP*TP)-3'; COMPND 13 CHAIN: D, G; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: NFI, TM_1865; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS HYPOXANTHINE, ENDONUCLEASE, ENDONUCLEASEV, HYDROLASE, INOSINE, DNA KEYWDS 2 DAMAGE, DNA REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR B.DALHUS,A.S.ARVAI,I.ROSNES,O.E.OLSEN,P.H.BACKE,I.ALSETH,H.GAO,W.CAO, AUTHOR 2 J.A.TAINER,M.BJORAS REVDAT 4 19-JUN-24 2W35 1 REMARK REVDAT 3 05-JUL-23 2W35 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 LINK ATOM REVDAT 2 21-APR-09 2W35 1 JRNL REMARK REVDAT 1 20-JAN-09 2W35 0 JRNL AUTH B.DALHUS,A.S.ARVAI,I.ROSNES,O.E.OLSEN,P.H.BACKE,I.ALSETH, JRNL AUTH 2 H.GAO,W.CAO,J.A.TAINER,M.BJORAS JRNL TITL STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF JRNL TITL 2 DEAMINATED ADENINE REPAIR. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 138 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19136958 JRNL DOI 10.1038/NSMB.1538 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.15 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) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 39299 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) : 0.259 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1967 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3574 REMARK 3 BIN R VALUE (WORKING SET) : 0.5640 REMARK 3 BIN FREE R VALUE : 0.5350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 196 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 : 3580 REMARK 3 NUCLEIC ACID ATOMS : 432 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : 0.37 REMARK 3 BSOL : 52.80 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 : INOSIN.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 : INOSIN.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 2W35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290035776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9185 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 : 39299 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.53200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.14600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 97.22500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.53200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.14600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.22500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.53200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.14600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 97.22500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.53200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.14600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 97.22500 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -0.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 BIOMT1 2 -1.000000 0.000000 0.000000 55.06400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, 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 BIOMT1 2 -1.000000 0.000000 0.000000 55.06400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 268.58400 REMARK 350 BIOMT3 2 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 PHE A 225 REMARK 465 PHE B 225 REMARK 465 DA C 1 REMARK 465 DT C 2 REMARK 465 DG C 3 REMARK 465 DC C 4 REMARK 465 DG C 5 REMARK 465 DG D 14 REMARK 465 DT D 15 REMARK 465 DA F 1 REMARK 465 DT F 2 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 LEU A 224 CA C O CB CG CD1 CD2 REMARK 470 LEU B 224 CA C O CB CG CD1 CD2 REMARK 470 DG F 3 P OP1 OP2 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 DA D 10 P DA D 10 OP3 -0.084 REMARK 500 DA G 10 P DA G 10 OP3 -0.085 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 ALA A 115 74.93 -69.80 REMARK 500 ARG A 153 -47.07 -21.61 REMARK 500 LYS A 222 -143.46 -68.22 REMARK 500 GLU B 72 113.05 -176.20 REMARK 500 CYS B 154 -1.04 83.29 REMARK 500 ASP B 161 75.91 -119.75 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 DC D 12 0.07 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2012 DISTANCE = 6.50 ANGSTROMS 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 MG A1224 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 110 OD1 93.9 REMARK 620 3 HOH A2024 O 100.6 164.9 REMARK 620 4 DG C 9 O3' 178.6 87.3 78.1 REMARK 620 5 HOH C2007 O 107.8 88.8 82.9 71.7 REMARK 620 6 HOH C2009 O 92.2 83.5 99.9 88.5 159.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1224 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 43 OD1 REMARK 620 2 ASP B 110 OD2 96.0 REMARK 620 3 HOH B2041 O 99.4 78.1 REMARK 620 4 DG F 9 O3' 172.5 81.3 86.9 REMARK 620 5 HOH F2004 O 104.3 155.6 110.9 76.8 REMARK 620 6 HOH F2005 O 106.7 77.2 145.6 65.9 84.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1224 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W36 RELATED DB: PDB REMARK 900 STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF REMARK 900 DEAMINATED ADENINE REPAIR DBREF 2W35 A 1 225 UNP Q9X2H9 NFI_THEMA 1 225 DBREF 2W35 B 1 225 UNP Q9X2H9 NFI_THEMA 1 225 DBREF 2W35 C 1 9 PDB 2W35 2W35 1 9 DBREF 2W35 D 10 15 PDB 2W35 2W35 10 15 DBREF 2W35 F 1 9 PDB 2W35 2W35 1 9 DBREF 2W35 G 10 15 PDB 2W35 2W35 10 15 SEQRES 1 A 225 MET ASP TYR ARG GLN LEU HIS ARG TRP ASP LEU PRO PRO SEQRES 2 A 225 GLU GLU ALA ILE LYS VAL GLN ASN GLU LEU ARG LYS LYS SEQRES 3 A 225 ILE LYS LEU THR PRO TYR GLU GLY GLU PRO GLU TYR VAL SEQRES 4 A 225 ALA GLY VAL ASP LEU SER PHE PRO GLY LYS GLU GLU GLY SEQRES 5 A 225 LEU ALA VAL ILE VAL VAL LEU GLU TYR PRO SER PHE LYS SEQRES 6 A 225 ILE LEU GLU VAL VAL SER GLU ARG GLY GLU ILE THR PHE SEQRES 7 A 225 PRO TYR ILE PRO GLY LEU LEU ALA PHE ARG GLU GLY PRO SEQRES 8 A 225 LEU PHE LEU LYS ALA TRP GLU LYS LEU ARG THR LYS PRO SEQRES 9 A 225 ASP VAL VAL VAL PHE ASP GLY GLN GLY LEU ALA HIS PRO SEQRES 10 A 225 ARG LYS LEU GLY ILE ALA SER HIS MET GLY LEU PHE ILE SEQRES 11 A 225 GLU ILE PRO THR ILE GLY VAL ALA LYS SER ARG LEU TYR SEQRES 12 A 225 GLY THR PHE LYS MET PRO GLU ASP LYS ARG CYS SER TRP SEQRES 13 A 225 SER TYR LEU TYR ASP GLY GLU GLU ILE ILE GLY CYS VAL SEQRES 14 A 225 ILE ARG THR LYS GLU GLY SER ALA PRO ILE PHE VAL SER SEQRES 15 A 225 PRO GLY HIS LEU MET ASP VAL GLU SER SER LYS ARG LEU SEQRES 16 A 225 ILE LYS ALA PHE THR LEU PRO GLY ARG ARG ILE PRO GLU SEQRES 17 A 225 PRO THR ARG LEU ALA HIS ILE TYR THR GLN ARG LEU LYS SEQRES 18 A 225 LYS GLY LEU PHE SEQRES 1 B 225 MET ASP TYR ARG GLN LEU HIS ARG TRP ASP LEU PRO PRO SEQRES 2 B 225 GLU GLU ALA ILE LYS VAL GLN ASN GLU LEU ARG LYS LYS SEQRES 3 B 225 ILE LYS LEU THR PRO TYR GLU GLY GLU PRO GLU TYR VAL SEQRES 4 B 225 ALA GLY VAL ASP LEU SER PHE PRO GLY LYS GLU GLU GLY SEQRES 5 B 225 LEU ALA VAL ILE VAL VAL LEU GLU TYR PRO SER PHE LYS SEQRES 6 B 225 ILE LEU GLU VAL VAL SER GLU ARG GLY GLU ILE THR PHE SEQRES 7 B 225 PRO TYR ILE PRO GLY LEU LEU ALA PHE ARG GLU GLY PRO SEQRES 8 B 225 LEU PHE LEU LYS ALA TRP GLU LYS LEU ARG THR LYS PRO SEQRES 9 B 225 ASP VAL VAL VAL PHE ASP GLY GLN GLY LEU ALA HIS PRO SEQRES 10 B 225 ARG LYS LEU GLY ILE ALA SER HIS MET GLY LEU PHE ILE SEQRES 11 B 225 GLU ILE PRO THR ILE GLY VAL ALA LYS SER ARG LEU TYR SEQRES 12 B 225 GLY THR PHE LYS MET PRO GLU ASP LYS ARG CYS SER TRP SEQRES 13 B 225 SER TYR LEU TYR ASP GLY GLU GLU ILE ILE GLY CYS VAL SEQRES 14 B 225 ILE ARG THR LYS GLU GLY SER ALA PRO ILE PHE VAL SER SEQRES 15 B 225 PRO GLY HIS LEU MET ASP VAL GLU SER SER LYS ARG LEU SEQRES 16 B 225 ILE LYS ALA PHE THR LEU PRO GLY ARG ARG ILE PRO GLU SEQRES 17 B 225 PRO THR ARG LEU ALA HIS ILE TYR THR GLN ARG LEU LYS SEQRES 18 B 225 LYS GLY LEU PHE SEQRES 1 C 9 DA DT DG DC DG DA DC DI DG SEQRES 1 D 6 DA DG DC DC DG DT SEQRES 1 F 9 DA DT DG DC DG DA DC DI DG SEQRES 1 G 6 DA DG DC DC DG DT HET MG A1224 1 HET MG B1224 1 HETNAM MG MAGNESIUM ION FORMUL 7 MG 2(MG 2+) FORMUL 9 HOH *216(H2 O) HELIX 1 1 PRO A 12 ARG A 24 1 13 HELIX 2 2 LYS A 25 ILE A 27 5 3 HELIX 3 3 LEU A 84 GLU A 98 1 15 HELIX 4 4 GLY A 121 GLU A 131 1 11 HELIX 5 5 ASP A 188 THR A 200 1 13 HELIX 6 6 PRO A 207 LYS A 222 1 16 HELIX 7 7 PRO B 12 ARG B 24 1 13 HELIX 8 8 LYS B 25 ILE B 27 5 3 HELIX 9 9 LEU B 85 GLU B 98 1 14 HELIX 10 10 GLY B 121 GLU B 131 1 11 HELIX 11 11 ASP B 188 THR B 200 1 13 HELIX 12 12 PRO B 207 LEU B 220 1 14 SHEET 1 AA 8 LYS A 65 GLU A 75 0 SHEET 2 AA 8 GLU A 51 GLU A 60 -1 O GLY A 52 N GLY A 74 SHEET 3 AA 8 TYR A 38 GLY A 48 -1 O VAL A 39 N LEU A 59 SHEET 4 AA 8 VAL A 106 PHE A 109 1 O VAL A 106 N ALA A 40 SHEET 5 AA 8 THR A 134 ALA A 138 1 O ILE A 135 N PHE A 109 SHEET 6 AA 8 ILE A 179 PRO A 183 -1 O PHE A 180 N ALA A 138 SHEET 7 AA 8 GLU A 164 ILE A 170 -1 O CYS A 168 N VAL A 181 SHEET 8 AA 8 TRP A 156 ASP A 161 -1 O SER A 157 N VAL A 169 SHEET 1 BA 8 LYS B 65 GLU B 75 0 SHEET 2 BA 8 GLU B 51 GLU B 60 -1 O GLY B 52 N GLY B 74 SHEET 3 BA 8 TYR B 38 GLY B 48 -1 O VAL B 39 N LEU B 59 SHEET 4 BA 8 VAL B 106 ASP B 110 1 O VAL B 106 N ALA B 40 SHEET 5 BA 8 THR B 134 ALA B 138 1 O ILE B 135 N PHE B 109 SHEET 6 BA 8 ILE B 179 PRO B 183 -1 O PHE B 180 N ALA B 138 SHEET 7 BA 8 GLU B 164 ILE B 170 -1 O CYS B 168 N VAL B 181 SHEET 8 BA 8 TRP B 156 ASP B 161 -1 O SER B 157 N VAL B 169 LINK OD1 ASP A 43 MG MG A1224 1555 1555 1.93 LINK OD1 ASP A 110 MG MG A1224 1555 1555 2.24 LINK MG MG A1224 O HOH A2024 1555 1555 2.24 LINK MG MG A1224 O3' DG C 9 1555 1555 1.95 LINK MG MG A1224 O HOH C2007 1555 1555 2.21 LINK MG MG A1224 O HOH C2009 1555 1555 2.02 LINK OD1 ASP B 43 MG MG B1224 1555 1555 1.89 LINK OD2 ASP B 110 MG MG B1224 1555 1555 2.19 LINK MG MG B1224 O HOH B2041 1555 1555 1.86 LINK MG MG B1224 O3' DG F 9 1555 1555 1.89 LINK MG MG B1224 O HOH F2004 1555 1555 2.16 LINK MG MG B1224 O HOH F2005 1555 1555 2.43 CISPEP 1 TYR A 61 PRO A 62 0 0.32 CISPEP 2 TYR B 61 PRO B 62 0 0.19 SITE 1 AC1 6 ASP A 43 ASP A 110 HOH A2024 DG C 9 SITE 2 AC1 6 HOH C2007 HOH C2009 SITE 1 AC2 6 ASP B 43 ASP B 110 HOH B2041 DG F 9 SITE 2 AC2 6 HOH F2004 HOH F2005 CRYST1 55.064 134.292 194.450 90.00 90.00 90.00 I 2 2 2 16 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 0.018161 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007446 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005143 0.00000