HEADER DNA BINDING PROTEIN 07-APR-20 6WH2 TITLE STRUCTURE OF THE C-TERMINAL BRCT DOMAIN OF HUMAN XRCC1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: X-RAY REPAIR CROSS COMPLEMENTING PROTEIN 1 VARIANT; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SECOND BRCT DOMAIN; COMPND 5 SYNONYM: XRCC1; COMPND 6 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 KEYWDS DNA LIGASE COMPLEX, DNA REPAIR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.POURFARJAM,T.ELLENBERGER,J.A.TAINER,A.E.TOMKINSON,I.K.KIM REVDAT 4 18-OCT-23 6WH2 1 REMARK REVDAT 3 20-JAN-21 6WH2 1 JRNL REVDAT 2 30-DEC-20 6WH2 1 JRNL REVDAT 1 02-DEC-20 6WH2 0 JRNL AUTH M.HAMMEL,I.RASHID,A.SVERZHINSKY,Y.POURFARJAM,M.S.TSAI, JRNL AUTH 2 T.ELLENBERGER,J.M.PASCAL,I.K.KIM,J.A.TAINER,A.E.TOMKINSON JRNL TITL AN ATYPICAL BRCT-BRCT INTERACTION WITH THE XRCC1 SCAFFOLD JRNL TITL 2 PROTEIN COMPACTS HUMAN DNA LIGASE III ALPHA WITHIN A JRNL TITL 3 FLEXIBLE DNA REPAIR COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 49 306 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33330937 JRNL DOI 10.1093/NAR/GKAA1188 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 8682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 867 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 5.1700 - 4.3837 1.00 1400 153 0.1759 0.1862 REMARK 3 2 4.3837 - 3.4810 1.00 1318 139 0.2049 0.2367 REMARK 3 3 3.4810 - 3.0414 1.00 1289 145 0.2500 0.2832 REMARK 3 4 3.0414 - 2.7635 1.00 1296 148 0.2737 0.3214 REMARK 3 5 2.7635 - 2.5655 1.00 1279 137 0.2978 0.3987 REMARK 3 6 2.5655 - 2.4143 0.97 1233 145 0.3132 0.3568 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.38 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1664 REMARK 3 ANGLE : 0.486 2255 REMARK 3 CHIRALITY : 0.042 221 REMARK 3 PLANARITY : 0.005 300 REMARK 3 DIHEDRAL : 3.214 980 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 538:632) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7371 -3.3916 26.3942 REMARK 3 T TENSOR REMARK 3 T11: 0.3302 T22: 0.3053 REMARK 3 T33: 0.3362 T12: 0.0174 REMARK 3 T13: 0.0203 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 3.7874 L22: 3.2653 REMARK 3 L33: 5.3389 L12: 1.1367 REMARK 3 L13: -0.1442 L23: -1.5593 REMARK 3 S TENSOR REMARK 3 S11: 0.0711 S12: 0.1286 S13: 0.1328 REMARK 3 S21: -0.1007 S22: -0.1153 S23: -0.0665 REMARK 3 S31: -0.1730 S32: 0.1262 S33: 0.0014 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 538:633) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9646 4.5187 -0.2502 REMARK 3 T TENSOR REMARK 3 T11: 0.3181 T22: 0.3221 REMARK 3 T33: 0.3671 T12: -0.0597 REMARK 3 T13: -0.0283 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 3.6071 L22: 2.2793 REMARK 3 L33: 5.8631 L12: 0.8557 REMARK 3 L13: 0.3743 L23: -0.2599 REMARK 3 S TENSOR REMARK 3 S11: 0.0220 S12: -0.1585 S13: -0.1066 REMARK 3 S21: -0.0276 S22: -0.0287 S23: -0.1172 REMARK 3 S31: 0.3215 S32: -0.1084 S33: 0.0065 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6WH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12712 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1CDZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-14% PEG 3350, 0.1M BIS-TRIS PH 5.5 REMARK 280 AND 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 19.48750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.62800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.17400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.62800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.48750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.17400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -19.48750 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 50.62800 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 ALA A 633 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 NH1 ARG A 610 O HOH A 701 2.01 REMARK 500 O ASP A 575 O HOH A 702 2.06 REMARK 500 OG SER A 578 O HOH A 703 2.07 REMARK 500 O HOH A 704 O HOH A 719 2.08 REMARK 500 NH1 ARG B 559 O HOH B 701 2.10 REMARK 500 OD1 ASN B 601 O HOH B 702 2.10 REMARK 500 O HOH A 722 O HOH A 723 2.10 REMARK 500 O TYR B 576 O HOH B 703 2.12 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 ASP B 541 44.53 -141.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 6WH2 A 538 633 UNP Q59HH7 Q59HH7_HUMAN 552 647 DBREF 6WH2 B 538 633 UNP Q59HH7 Q59HH7_HUMAN 552 647 SEQRES 1 A 96 GLU LEU PRO ASP PHE PHE GLN GLY LYS HIS PHE PHE LEU SEQRES 2 A 96 TYR GLY GLU PHE PRO GLY ASP GLU ARG ARG LYS LEU ILE SEQRES 3 A 96 ARG TYR VAL THR ALA PHE ASN GLY GLU LEU GLU ASP TYR SEQRES 4 A 96 MET SER ASP ARG VAL GLN PHE VAL ILE THR ALA GLN GLU SEQRES 5 A 96 TRP ASP PRO SER PHE GLU GLU ALA LEU MET ASP ASN PRO SEQRES 6 A 96 SER LEU ALA PHE VAL ARG PRO ARG TRP ILE TYR SER CYS SEQRES 7 A 96 ASN GLU LYS GLN LYS LEU LEU PRO HIS GLN LEU TYR GLY SEQRES 8 A 96 VAL VAL PRO GLN ALA SEQRES 1 B 96 GLU LEU PRO ASP PHE PHE GLN GLY LYS HIS PHE PHE LEU SEQRES 2 B 96 TYR GLY GLU PHE PRO GLY ASP GLU ARG ARG LYS LEU ILE SEQRES 3 B 96 ARG TYR VAL THR ALA PHE ASN GLY GLU LEU GLU ASP TYR SEQRES 4 B 96 MET SER ASP ARG VAL GLN PHE VAL ILE THR ALA GLN GLU SEQRES 5 B 96 TRP ASP PRO SER PHE GLU GLU ALA LEU MET ASP ASN PRO SEQRES 6 B 96 SER LEU ALA PHE VAL ARG PRO ARG TRP ILE TYR SER CYS SEQRES 7 B 96 ASN GLU LYS GLN LYS LEU LEU PRO HIS GLN LEU TYR GLY SEQRES 8 B 96 VAL VAL PRO GLN ALA FORMUL 3 HOH *53(H2 O) HELIX 1 AA1 ASP A 557 PHE A 569 1 13 HELIX 2 AA2 ASP A 591 ASN A 601 1 11 HELIX 3 AA3 ARG A 608 GLN A 619 1 12 HELIX 4 AA4 PRO A 623 GLY A 628 5 6 HELIX 5 AA5 ASP B 557 PHE B 569 1 13 HELIX 6 AA6 ASP B 591 ASN B 601 1 11 HELIX 7 AA7 PRO B 609 GLN B 619 1 11 HELIX 8 AA8 PRO B 623 GLY B 628 5 6 SHEET 1 AA1 4 GLU A 572 LEU A 573 0 SHEET 2 AA1 4 HIS A 547 TYR A 551 1 N PHE A 548 O GLU A 572 SHEET 3 AA1 4 PHE A 583 THR A 586 1 O ILE A 585 N TYR A 551 SHEET 4 AA1 4 ALA A 605 VAL A 607 1 O ALA A 605 N VAL A 584 SHEET 1 AA2 4 GLU B 572 LEU B 573 0 SHEET 2 AA2 4 HIS B 547 LEU B 550 1 N PHE B 548 O GLU B 572 SHEET 3 AA2 4 PHE B 583 ILE B 585 1 O ILE B 585 N PHE B 549 SHEET 4 AA2 4 ALA B 605 VAL B 607 1 O ALA B 605 N VAL B 584 CRYST1 38.975 54.348 101.256 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 0.025657 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009876 0.00000