PDB Short entry for 2W3O HEADER HYDROLASE,TRANSFERASE/PEPTIDE 13-NOV-08 2W3O TITLE CRYSTAL STRUCTURE OF THE HUMAN PNKP FHA DOMAIN IN COMPLEX WITH AN TITLE 2 XRCC1-DERIVED PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FHA DOMAIN, RESIDUES 1-110; COMPND 5 SYNONYM: FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE, DNA 5'- COMPND 6 KINASE/3'-PHOSPHATASE, POLYNUCLEOTIDE 5'-HYDROXYL-KINASE, COMPND 7 POLYNUCLEOTIDE 3'-PHOSPHATASE; COMPND 8 EC: 3.1.3.32, 2.7.1.78; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DNA REPAIR PROTEIN XRCC1; COMPND 13 CHAIN: C, D; COMPND 14 FRAGMENT: RESIDUES 515-522; COMPND 15 SYNONYM: X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 1, XRCC1-DERIVED COMPND 16 PHOSPHOPEPTIDE; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTWO-E; SOURCE 9 OTHER_DETAILS: SYNTHETIC GENE; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE, TRANSFERASE/PEPTIDE, FHA, PNKP, XRCC1, KINASE, NUCLEUS, KEYWDS 2 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE, DNA DAMAGE, DNA REPAIR, KEYWDS 3 TRANSFERASE, ATP-BINDING, MULTIFUNCTIONAL ENZYME, POLYMORPHISM, KEYWDS 4 PHOSPHOPROTEIN, PHOSPHO- PEPTIDE, NUCLEOTIDE-BINDING, BASE EXCISION KEYWDS 5 REPAIR, TRANSFERASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.W.OLIVER,A.A.E.ALI,L.H.PEARL REVDAT 3 13-DEC-23 2W3O 1 LINK REVDAT 2 24-MAR-09 2W3O 1 JRNL REVDAT 1 03-FEB-09 2W3O 0 JRNL AUTH A.A.E.ALI,R.M.JUKES,L.H.PEARL,A.W.OLIVER JRNL TITL SPECIFIC RECOGNITION OF A MULTIPLY PHOSPHORYLATED MOTIF IN JRNL TITL 2 THE DNA REPAIR SCAFFOLD XRCC1 BY THE FHA DOMAIN OF HUMAN JRNL TITL 3 PNK. JRNL REF NUCLEIC ACIDS RES. V. 37 1701 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19155274 JRNL DOI 10.1093/NAR/GKN1086 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 18234 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 + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 977 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1271 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1634 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.44000 REMARK 3 B12 (A**2) : -0.15000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.452 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1692 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2328 ; 1.720 ; 2.022 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 6.316 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;33.061 ;24.706 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 263 ;13.635 ;15.228 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.591 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 269 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1266 ; 0.008 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1087 ; 1.052 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1760 ; 1.817 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 605 ; 2.659 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 564 ; 4.349 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2W3O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290038111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2080 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : KIRKPATRICK BAEZ BIMORPH MIRROR REMARK 200 PAIR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19211 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 38.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.370 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.12 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.430 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 2BRF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, REMARK 280 28% W/V PEG 4000, 0.2 M NDSB-221 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -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 0.00000 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 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2020 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2011 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2051 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LEU 99 TO GLU REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LEU 99 TO GLU 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 GLY A -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLU A 3 REMARK 465 VAL A 4 REMARK 465 GLU A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLU A 108 REMARK 465 THR A 109 REMARK 465 ARG A 110 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 GLU B 3 REMARK 465 VAL B 4 REMARK 465 GLU B 5 REMARK 465 ALA B 6 REMARK 465 PRO B 7 REMARK 465 THR B 109 REMARK 465 ARG B 110 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 ASP A 27 CG OD1 OD2 REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 ASP B 27 OD1 OD2 REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 GLU B 108 CG CD OE1 OE2 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 C 2005 O HOH C 2006 1.77 REMARK 500 O HOH A 2100 O HOH A 2103 2.06 REMARK 500 O1P SEP D 518 O HOH D 2010 2.14 REMARK 500 O VAL A 32 O HOH A 2053 2.16 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 GLU A 18 -136.29 -99.98 REMARK 500 HIS A 100 66.90 67.85 REMARK 500 GLU B 18 -135.37 -101.41 REMARK 500 HIS B 100 70.62 64.77 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 A2024 DISTANCE = 6.97 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 CA A1109 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 58 O REMARK 620 2 HOH A2074 O 92.9 REMARK 620 3 HOH A2088 O 82.7 171.8 REMARK 620 4 HOH A2089 O 67.6 88.5 96.3 REMARK 620 5 HOH A2091 O 177.4 89.5 95.0 111.5 REMARK 620 6 HOH A2120 O 84.3 80.0 92.5 149.0 97.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1108 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 60 NH1 REMARK 620 2 HOH A2052 O 113.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1109 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 56 OD1 REMARK 620 2 HOH B2038 O 86.4 REMARK 620 3 HOH B2070 O 74.4 148.7 REMARK 620 4 HOH B2072 O 72.2 73.4 121.5 REMARK 620 5 HOH B2107 O 120.0 140.9 70.2 87.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1110 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 58 O REMARK 620 2 HOH B2017 O 176.1 REMARK 620 3 HOH B2060 O 96.4 81.2 REMARK 620 4 HOH B2071 O 87.7 94.5 173.8 REMARK 620 5 HOH B2073 O 73.1 109.9 92.7 93.0 REMARK 620 6 HOH B2106 O 83.0 93.7 83.0 92.8 155.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C1008 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SEP C 518 O1P REMARK 620 2 HOH C2009 O 91.4 REMARK 620 3 SEP D 518 OG 78.5 87.1 REMARK 620 4 TPO D 519 O2P 156.9 86.1 78.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D1008 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SEP C 518 O3P REMARK 620 2 TPO C 519 O2P 79.0 REMARK 620 3 SEP D 518 O3P 87.2 165.5 REMARK 620 4 HOH D2008 O 74.2 84.2 88.0 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 C1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1110 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CDZ RELATED DB: PDB REMARK 900 BRCT DOMAIN FROM DNA-REPAIR PROTEIN XRCC1 REMARK 900 RELATED ID: 1XNT RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIRPROTEIN REMARK 900 XRCC1-N-TERMINAL DOMAIN REMARK 900 RELATED ID: 2BRF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FHA DOMAIN OF HUMAN POLYNUCLEOTIDE KINASE REMARK 900 3' PHOSPHATASE REMARK 900 RELATED ID: 1XNA RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIRPROTEIN REMARK 900 XRCC1-N-TERMINAL DOMAIN REMARK 900 RELATED ID: 2D8M RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE FIRST BRCT DOMAIN OF DNA-REPAIRPROTEIN REMARK 900 XRCC1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE THAT WAS SYNTHESIZED WAS TAKEN FROM THAT REPORTED IN REMARK 999 "MOLECULAR CLONING OF THE HUMAN GENE, PNKP, ENCODING A POLYNUCLEOTID REMARK 999 KINASE 3'-PHOSPHATASE AND EVIDENCE FOR ITS ROLE IN REPAIR OF DNA REMARK 999 STRAND BREAKS CAUSED BY OXIDATIVE DAMAGE." JILANI A., RAMOTAR D., REMARK 999 SLACK C., ONG C., YANG X.M., SCHERER S.W., LASKO D.D. J. BIOL. CHEM. REMARK 999 274:24176-24186(1999), WHICH HAS A GLYCINE AT POSITION 18 INSTEAD OF REMARK 999 A GLUTAMIC ACID. DBREF 2W3O A -2 0 PDB 2W3O 2W3O -2 0 DBREF 2W3O A 1 110 UNP Q96T60 PNKP_HUMAN 1 110 DBREF 2W3O B -2 0 PDB 2W3O 2W3O -2 0 DBREF 2W3O B 1 110 UNP Q96T60 PNKP_HUMAN 1 110 DBREF 2W3O C 515 522 UNP P18887 XRCC1_HUMAN 515 522 DBREF 2W3O D 515 522 UNP P18887 XRCC1_HUMAN 515 522 SEQADV 2W3O GLU A 18 UNP Q96T60 GLY 18 SEE REMARK 999 SEQADV 2W3O GLU A 99 UNP Q96T60 LEU 99 ENGINEERED MUTATION SEQADV 2W3O GLU B 18 UNP Q96T60 GLY 18 SEE REMARK 999 SEQADV 2W3O GLU B 99 UNP Q96T60 LEU 99 ENGINEERED MUTATION SEQRES 1 A 113 GLY PRO HIS MET GLY GLU VAL GLU ALA PRO GLY ARG LEU SEQRES 2 A 113 TRP LEU GLU SER PRO PRO GLY GLU ALA PRO PRO ILE PHE SEQRES 3 A 113 LEU PRO SER ASP GLY GLN ALA LEU VAL LEU GLY ARG GLY SEQRES 4 A 113 PRO LEU THR GLN VAL THR ASP ARG LYS CYS SER ARG THR SEQRES 5 A 113 GLN VAL GLU LEU VAL ALA ASP PRO GLU THR ARG THR VAL SEQRES 6 A 113 ALA VAL LYS GLN LEU GLY VAL ASN PRO SER THR THR GLY SEQRES 7 A 113 THR GLN GLU LEU LYS PRO GLY LEU GLU GLY SER LEU GLY SEQRES 8 A 113 VAL GLY ASP THR LEU TYR LEU VAL ASN GLY GLU HIS PRO SEQRES 9 A 113 LEU THR LEU ARG TRP GLU GLU THR ARG SEQRES 1 B 113 GLY PRO HIS MET GLY GLU VAL GLU ALA PRO GLY ARG LEU SEQRES 2 B 113 TRP LEU GLU SER PRO PRO GLY GLU ALA PRO PRO ILE PHE SEQRES 3 B 113 LEU PRO SER ASP GLY GLN ALA LEU VAL LEU GLY ARG GLY SEQRES 4 B 113 PRO LEU THR GLN VAL THR ASP ARG LYS CYS SER ARG THR SEQRES 5 B 113 GLN VAL GLU LEU VAL ALA ASP PRO GLU THR ARG THR VAL SEQRES 6 B 113 ALA VAL LYS GLN LEU GLY VAL ASN PRO SER THR THR GLY SEQRES 7 B 113 THR GLN GLU LEU LYS PRO GLY LEU GLU GLY SER LEU GLY SEQRES 8 B 113 VAL GLY ASP THR LEU TYR LEU VAL ASN GLY GLU HIS PRO SEQRES 9 B 113 LEU THR LEU ARG TRP GLU GLU THR ARG SEQRES 1 C 8 TYR ALA GLY SEP TPO ASP GLU ASN SEQRES 1 D 8 TYR ALA GLY SEP TPO ASP GLU ASN MODRES 2W3O SEP C 518 SER PHOSPHOSERINE MODRES 2W3O TPO C 519 THR PHOSPHOTHREONINE MODRES 2W3O SEP D 518 SER PHOSPHOSERINE MODRES 2W3O TPO D 519 THR PHOSPHOTHREONINE HET SEP C 518 17 HET TPO C 519 11 HET SEP D 518 17 HET TPO D 519 11 HET CA A1108 1 HET CA A1109 1 HET CA B1109 1 HET CA B1110 1 HET CA C1008 1 HET CA D1008 1 HETNAM SEP PHOSPHOSERINE HETNAM TPO PHOSPHOTHREONINE HETNAM CA CALCIUM ION HETSYN SEP PHOSPHONOSERINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 3 SEP 2(C3 H8 N O6 P) FORMUL 3 TPO 2(C4 H10 N O6 P) FORMUL 5 CA 6(CA 2+) FORMUL 11 HOH *286(H2 O) SHEET 1 AA 6 ILE A 22 PHE A 23 0 SHEET 2 AA 6 ARG A 9 GLU A 13 -1 O LEU A 12 N ILE A 22 SHEET 3 AA 6 GLU A 99 GLU A 107 -1 O THR A 103 N GLU A 13 SHEET 4 AA 6 THR A 92 VAL A 96 -1 O LEU A 93 N LEU A 102 SHEET 5 AA 6 THR A 73 THR A 74 -1 O THR A 73 N TYR A 94 SHEET 6 AA 6 GLN A 77 GLU A 78 -1 O GLN A 77 N THR A 74 SHEET 1 AB 4 ALA A 30 LEU A 33 0 SHEET 2 AB 4 VAL A 51 ASP A 56 -1 O VAL A 51 N LEU A 33 SHEET 3 AB 4 THR A 61 GLN A 66 -1 O THR A 61 N ASP A 56 SHEET 4 AB 4 GLU A 84 GLY A 88 -1 O GLY A 85 N VAL A 64 SHEET 1 BA 6 ILE B 22 PHE B 23 0 SHEET 2 BA 6 ARG B 9 GLU B 13 -1 O LEU B 12 N ILE B 22 SHEET 3 BA 6 GLU B 99 GLU B 107 -1 O THR B 103 N GLU B 13 SHEET 4 BA 6 THR B 92 VAL B 96 -1 O LEU B 93 N LEU B 102 SHEET 5 BA 6 THR B 73 THR B 74 -1 O THR B 73 N TYR B 94 SHEET 6 BA 6 GLN B 77 GLU B 78 -1 O GLN B 77 N THR B 74 SHEET 1 BB 4 ALA B 30 LEU B 33 0 SHEET 2 BB 4 VAL B 51 ASP B 56 -1 O VAL B 51 N LEU B 33 SHEET 3 BB 4 THR B 61 GLN B 66 -1 O THR B 61 N ASP B 56 SHEET 4 BB 4 GLU B 84 GLY B 88 -1 O GLY B 85 N VAL B 64 LINK C GLY C 517 N SEP C 518 1555 1555 1.34 LINK C SEP C 518 N TPO C 519 1555 1555 1.33 LINK C TPO C 519 N ASP C 520 1555 1555 1.33 LINK C GLY D 517 N SEP D 518 1555 1555 1.34 LINK C SEP D 518 N TPO D 519 1555 1555 1.33 LINK C TPO D 519 N ASP D 520 1555 1555 1.33 LINK O GLU A 58 CA CA A1109 1555 1555 2.81 LINK NH1 ARG A 60 CA CA A1108 1555 1555 3.05 LINK CA CA A1108 O HOH A2052 1555 1555 2.53 LINK CA CA A1109 O HOH A2074 1555 2645 3.13 LINK CA CA A1109 O HOH A2088 1555 1555 2.51 LINK CA CA A1109 O HOH A2089 1555 1555 2.29 LINK CA CA A1109 O HOH A2091 1555 1555 2.63 LINK CA CA A1109 O HOH A2120 1555 2645 2.41 LINK OD1 ASP B 56 CA CA B1109 1555 1555 2.81 LINK O GLU B 58 CA CA B1110 1555 1555 2.75 LINK CA CA B1109 O HOH B2038 1555 1555 2.98 LINK CA CA B1109 O HOH B2070 1555 1555 2.42 LINK CA CA B1109 O HOH B2072 1555 1555 2.80 LINK CA CA B1109 O HOH B2107 1555 3555 2.55 LINK CA CA B1110 O HOH B2017 1555 1555 2.58 LINK CA CA B1110 O HOH B2060 1555 3555 2.87 LINK CA CA B1110 O HOH B2071 1555 1555 2.48 LINK CA CA B1110 O HOH B2073 1555 1555 2.34 LINK CA CA B1110 O HOH B2106 1555 3555 2.61 LINK O1PBSEP C 518 CA CA C1008 1555 1555 2.33 LINK O3PBSEP C 518 CA CA D1008 1555 1555 3.05 LINK O2P TPO C 519 CA CA D1008 1555 1555 2.34 LINK CA CA C1008 O HOH C2009 1555 1555 2.36 LINK CA CA C1008 OG BSEP D 518 1555 1555 3.03 LINK CA CA C1008 O2P TPO D 519 1555 1555 2.41 LINK O3PBSEP D 518 CA CA D1008 1555 1555 2.09 LINK CA CA D1008 O HOH D2008 1555 1555 2.82 SITE 1 AC1 4 SEP C 518 HOH C2009 SEP D 518 TPO D 519 SITE 1 AC2 2 ARG A 60 HOH A2052 SITE 1 AC3 4 SEP C 518 TPO C 519 SEP D 518 HOH D2008 SITE 1 AC4 5 ASP B 56 HOH B2038 HOH B2070 HOH B2072 SITE 2 AC4 5 HOH B2107 SITE 1 AC5 5 GLU A 58 HOH A2088 HOH A2089 HOH A2091 SITE 2 AC5 5 HOH A2120 SITE 1 AC6 6 GLU B 58 HOH B2017 HOH B2060 HOH B2071 SITE 2 AC6 6 HOH B2073 HOH B2106 CRYST1 56.900 56.900 62.770 90.00 90.00 120.00 P 3 6 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 0.017575 0.010147 0.000000 0.00000 SCALE2 0.000000 0.020293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015931 0.00000