HEADER DNA BINDING PROTEIN 21-OCT-10 3PC6 TITLE X-RAY CRYSTAL STRUCTURE OF THE SECOND XRCC1 BRCT DOMAIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN XRCC1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: XRCC1 SECOND BRCT DOMAIN (UNP RESIDUES 534-630); COMPND 5 SYNONYM: X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: XRCC-1, XRCC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS DNA REPAIR, BRCT DOMAIN, PROTEIN:PROTEIN INTERACTIONS, DNA LIGASE KEYWDS 2 III-ALPHA BRCT2 DOMAIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.CUNEO,J.M.KRAHN,R.E.LONDON REVDAT 4 06-SEP-23 3PC6 1 SEQADV REVDAT 3 08-NOV-17 3PC6 1 REMARK REVDAT 2 02-NOV-11 3PC6 1 JRNL VERSN REVDAT 1 15-JUN-11 3PC6 0 JRNL AUTH M.J.CUNEO,S.A.GABEL,J.M.KRAHN,M.A.RICKER,R.E.LONDON JRNL TITL THE STRUCTURAL BASIS FOR PARTITIONING OF THE XRCC1/DNA JRNL TITL 2 LIGASE III-{ALPHA} BRCT-MEDIATED DIMER COMPLEXES. JRNL REF NUCLEIC ACIDS RES. V. 39 7816 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21652643 JRNL DOI 10.1093/NAR/GKR419 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 20081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1033 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 37.6325 - 3.6321 1.00 2963 139 0.1711 0.2053 REMARK 3 2 3.6321 - 2.8833 1.00 2828 152 0.1634 0.2013 REMARK 3 3 2.8833 - 2.5189 1.00 2771 167 0.1936 0.2226 REMARK 3 4 2.5189 - 2.2886 1.00 2749 157 0.1893 0.2627 REMARK 3 5 2.2886 - 2.1246 0.99 2754 138 0.1774 0.2522 REMARK 3 6 2.1246 - 1.9993 0.97 2655 145 0.1896 0.2147 REMARK 3 7 1.9993 - 1.9000 0.85 2328 135 0.2060 0.2917 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 25.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.59940 REMARK 3 B22 (A**2) : -0.37940 REMARK 3 B33 (A**2) : -8.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 1831 REMARK 3 ANGLE : 0.863 2498 REMARK 3 CHIRALITY : 0.068 242 REMARK 3 PLANARITY : 0.004 337 REMARK 3 DIHEDRAL : 16.095 662 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3PC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20146 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.23100 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1CDZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6M NAFORMATE, 0.2M NAHEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 22.11500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.19000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.19000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.11500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.42500 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 MET A 534 REMARK 465 PRO A 535 REMARK 465 HIS A 635 REMARK 465 HIS A 636 REMARK 465 HIS A 637 REMARK 465 MET B 534 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 GLU A 542 CD OE1 OE2 REMARK 470 GLU A 587 CD OE1 OE2 REMARK 470 GLU A 594 CG CD OE1 OE2 REMARK 470 PRO B 535 N CB CG CD REMARK 470 GLU B 536 CD OE1 OE2 REMARK 470 ASP B 555 CG OD1 OD2 REMARK 470 GLU B 570 CD OE1 OE2 REMARK 470 GLU B 577 CG CD OE1 OE2 REMARK 470 GLU B 587 CG CD OE1 OE2 REMARK 470 GLU B 615 CD OE1 OE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PC7 RELATED DB: PDB REMARK 900 RELATED ID: 3PC8 RELATED DB: PDB REMARK 900 RELATED ID: 3QVG RELATED DB: PDB DBREF 3PC6 A 535 631 UNP Q60596 XRCC1_MOUSE 535 631 DBREF 3PC6 B 535 631 UNP Q60596 XRCC1_MOUSE 535 631 SEQADV 3PC6 MET A 534 UNP Q60596 INITIATING METHIONINE SEQADV 3PC6 HIS A 632 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS A 633 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS A 634 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS A 635 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS A 636 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS A 637 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 MET B 534 UNP Q60596 INITIATING METHIONINE SEQADV 3PC6 HIS B 632 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS B 633 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS B 634 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS B 635 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS B 636 UNP Q60596 EXPRESSION TAG SEQADV 3PC6 HIS B 637 UNP Q60596 EXPRESSION TAG SEQRES 1 A 104 MET PRO GLU LEU PRO ASP PHE PHE GLU GLY LYS HIS PHE SEQRES 2 A 104 PHE LEU TYR GLY GLU PHE PRO GLY ASP GLU ARG ARG ARG SEQRES 3 A 104 LEU ILE ARG TYR VAL THR ALA PHE ASN GLY GLU LEU GLU SEQRES 4 A 104 ASP TYR MET ASN GLU ARG VAL GLN PHE VAL ILE THR ALA SEQRES 5 A 104 GLN GLU TRP ASP PRO ASN PHE GLU GLU ALA LEU MET GLU SEQRES 6 A 104 ASN PRO SER LEU ALA PHE VAL ARG PRO ARG TRP ILE TYR SEQRES 7 A 104 SER CYS ASN GLU LYS GLN LYS LEU LEU PRO HIS GLN LEU SEQRES 8 A 104 TYR GLY VAL VAL PRO GLN ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 104 MET PRO GLU LEU PRO ASP PHE PHE GLU GLY LYS HIS PHE SEQRES 2 B 104 PHE LEU TYR GLY GLU PHE PRO GLY ASP GLU ARG ARG ARG SEQRES 3 B 104 LEU ILE ARG TYR VAL THR ALA PHE ASN GLY GLU LEU GLU SEQRES 4 B 104 ASP TYR MET ASN GLU ARG VAL GLN PHE VAL ILE THR ALA SEQRES 5 B 104 GLN GLU TRP ASP PRO ASN PHE GLU GLU ALA LEU MET GLU SEQRES 6 B 104 ASN PRO SER LEU ALA PHE VAL ARG PRO ARG TRP ILE TYR SEQRES 7 B 104 SER CYS ASN GLU LYS GLN LYS LEU LEU PRO HIS GLN LEU SEQRES 8 B 104 TYR GLY VAL VAL PRO GLN ALA HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *182(H2 O) HELIX 1 1 ASP A 555 PHE A 567 1 13 HELIX 2 2 ASP A 589 MET A 597 1 9 HELIX 3 3 ARG A 606 GLN A 617 1 12 HELIX 4 4 PRO A 621 GLY A 626 5 6 HELIX 5 5 GLN A 630 HIS A 634 5 5 HELIX 6 6 ASP B 555 PHE B 567 1 13 HELIX 7 7 ASN B 591 ASN B 599 1 9 HELIX 8 8 PRO B 607 GLN B 617 1 11 HELIX 9 9 PRO B 621 GLY B 626 5 6 SHEET 1 A 4 GLU A 570 LEU A 571 0 SHEET 2 A 4 HIS A 545 TYR A 549 1 N PHE A 546 O GLU A 570 SHEET 3 A 4 PHE A 581 THR A 584 1 O ILE A 583 N TYR A 549 SHEET 4 A 4 ALA A 603 VAL A 605 1 O ALA A 603 N VAL A 582 SHEET 1 B 4 GLU B 570 LEU B 571 0 SHEET 2 B 4 HIS B 545 TYR B 549 1 N PHE B 546 O GLU B 570 SHEET 3 B 4 PHE B 581 THR B 584 1 O ILE B 583 N TYR B 549 SHEET 4 B 4 ALA B 603 VAL B 605 1 O ALA B 603 N VAL B 582 CRYST1 44.230 56.850 100.380 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 0.022609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009962 0.00000