HEADER CELL CYCLE 06-OCT-11 3U3Z TITLE STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN TITLE 2 COMPLEX WITH AN H2A.X PEPTIDE PHOSPHORYLATED AT SER139 AND TYR142 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROCEPHALIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TANDEM BRCT DOMAINS (BRCT2-BRCT3, UNP RESIDUES 640-835); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H2A.X PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MCPH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTEV; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS DNA REPAIR, CELL CYCLE REGULATION, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR N.SINGH,J.R.THOMPSON,A.HEROUX,G.MER REVDAT 5 06-DEC-23 3U3Z 1 REMARK REVDAT 4 13-SEP-23 3U3Z 1 REMARK SEQADV LINK REVDAT 3 19-SEP-12 3U3Z 1 JRNL REVDAT 2 29-AUG-12 3U3Z 1 JRNL REVDAT 1 25-JUL-12 3U3Z 0 JRNL AUTH N.SINGH,H.BASNET,T.D.WILTSHIRE,D.H.MOHAMMAD,J.R.THOMPSON, JRNL AUTH 2 A.HEROUX,M.V.BOTUYAN,M.B.YAFFE,F.J.COUCH,M.G.ROSENFELD,G.MER JRNL TITL DUAL RECOGNITION OF PHOSPHOSERINE AND PHOSPHOTYROSINE IN JRNL TITL 2 HISTONE VARIANT H2A.X BY DNA DAMAGE RESPONSE PROTEIN MCPH1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 14381 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22908299 JRNL DOI 10.1073/PNAS.1212366109 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 29928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.730 REMARK 3 FREE R VALUE TEST SET COUNT : 517 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 23.7910 - 2.3850 0.98 7481 130 0.1340 0.1572 REMARK 3 2 2.3850 - 1.8933 1.00 7509 142 0.1032 0.1649 REMARK 3 3 1.8933 - 1.6541 0.99 7385 135 0.1194 0.2027 REMARK 3 4 1.6541 - 1.5000 0.94 7036 110 0.1486 0.2009 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 : 0.40 REMARK 3 B_SOL : 60.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 : 0.005 1641 REMARK 3 ANGLE : 1.071 2256 REMARK 3 CHIRALITY : 0.057 254 REMARK 3 PLANARITY : 0.005 281 REMARK 3 DIHEDRAL : 14.007 620 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 3U3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SAGITTAL FOCUSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 3SZM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG3350, 0.03 M CITRIC ACID, 0.07 REMARK 280 M BIS-TRIS-PROPANE, PH 7.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.26850 REMARK 290 SMTRY3 2 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: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 GLY A 637 REMARK 465 HIS A 638 REMARK 465 MET A 639 REMARK 465 SER A 640 REMARK 465 GLY A 641 REMARK 465 ARG A 642 REMARK 465 GLY A 643 REMARK 465 LYS A 644 REMARK 465 LYS A 645 REMARK 465 GLN A 835 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 LYS A 671 -160.58 62.92 REMARK 500 ALA A 748 -72.16 -70.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2 DBREF 3U3Z A 640 835 UNP Q8NEM0 MCPH1_HUMAN 640 835 DBREF 3U3Z B 1 4 PDB 3U3Z 3U3Z 1 4 SEQADV 3U3Z GLY A 637 UNP Q8NEM0 EXPRESSION TAG SEQADV 3U3Z HIS A 638 UNP Q8NEM0 EXPRESSION TAG SEQADV 3U3Z MET A 639 UNP Q8NEM0 EXPRESSION TAG SEQRES 1 A 199 GLY HIS MET SER GLY ARG GLY LYS LYS PRO THR ARG THR SEQRES 2 A 199 LEU VAL MET THR SER MET PRO SER GLU LYS GLN ASN VAL SEQRES 3 A 199 VAL ILE GLN VAL VAL ASP LYS LEU LYS GLY PHE SER ILE SEQRES 4 A 199 ALA PRO ASP VAL CYS GLU THR THR THR HIS VAL LEU SER SEQRES 5 A 199 GLY LYS PRO LEU ARG THR LEU ASN VAL LEU LEU GLY ILE SEQRES 6 A 199 ALA ARG GLY CYS TRP VAL LEU SER TYR ASP TRP VAL LEU SEQRES 7 A 199 TRP SER LEU GLU LEU GLY HIS TRP ILE SER GLU GLU PRO SEQRES 8 A 199 PHE GLU LEU SER HIS HIS PHE PRO ALA ALA PRO LEU CYS SEQRES 9 A 199 ARG SER GLU CYS HIS LEU SER ALA GLY PRO TYR ARG GLY SEQRES 10 A 199 THR LEU PHE ALA ASP GLN PRO VAL MET PHE VAL SER PRO SEQRES 11 A 199 ALA SER SER PRO PRO VAL ALA LYS LEU CYS GLU LEU VAL SEQRES 12 A 199 HIS LEU CYS GLY GLY ARG VAL SER GLN VAL PRO ARG GLN SEQRES 13 A 199 ALA SER ILE VAL ILE GLY PRO TYR SER GLY LYS LYS LYS SEQRES 14 A 199 ALA THR VAL LYS TYR LEU SER GLU LYS TRP VAL LEU ASP SEQRES 15 A 199 SER ILE THR GLN HIS LYS VAL CYS ALA PRO GLU ASN TYR SEQRES 16 A 199 LEU LEU SER GLN SEQRES 1 B 4 SEP GLN GLU PTR MODRES 3U3Z SEP B 1 SER PHOSPHOSERINE MODRES 3U3Z PTR B 4 TYR O-PHOSPHOTYROSINE HET SEP B 1 10 HET PTR B 4 31 HET GOL A 1 7 HET GOL A 2 6 HETNAM SEP PHOSPHOSERINE HETNAM PTR O-PHOSPHOTYROSINE HETNAM GOL GLYCEROL HETSYN SEP PHOSPHONOSERINE HETSYN PTR PHOSPHONOTYROSINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SEP C3 H8 N O6 P FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *279(H2 O) HELIX 1 1 PRO A 656 LYS A 671 1 16 HELIX 2 2 THR A 694 ARG A 703 1 10 HELIX 3 3 TYR A 710 GLY A 720 1 11 HELIX 4 4 GLU A 725 GLU A 729 5 5 HELIX 5 5 PRO A 735 SER A 747 1 13 HELIX 6 6 PRO A 771 CYS A 782 1 12 HELIX 7 7 VAL A 789 ALA A 793 5 5 HELIX 8 8 SER A 812 HIS A 823 1 12 HELIX 9 9 ALA A 827 LEU A 832 5 6 SHEET 1 A 4 SER A 674 ALA A 676 0 SHEET 2 A 4 THR A 649 THR A 653 1 N LEU A 650 O ALA A 676 SHEET 3 A 4 THR A 683 SER A 688 1 O LEU A 687 N VAL A 651 SHEET 4 A 4 TRP A 706 SER A 709 1 O TRP A 706 N VAL A 686 SHEET 1 B 3 MET A 762 VAL A 764 0 SHEET 2 B 3 ILE A 795 ILE A 797 1 O ILE A 797 N PHE A 763 SHEET 3 B 3 LYS A 809 LEU A 811 1 O LYS A 809 N VAL A 796 LINK C SEP B 1 N GLN B 2 1555 1555 1.33 LINK C GLU B 3 N PTR B 4 1555 1555 1.33 CISPEP 1 SER A 769 PRO A 770 0 5.99 SITE 1 AC1 9 HOH A 78 HOH A 200 PRO A 727 SER A 765 SITE 2 AC1 9 ALA A 767 PRO A 799 TYR A 800 SER A 801 SITE 3 AC1 9 GLY A 802 SITE 1 AC2 3 LEU A 714 TRP A 715 GLU A 718 CRYST1 37.689 46.537 55.778 90.00 97.07 90.00 P 1 21 1 2 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 0.026533 0.000000 0.003291 0.00000 SCALE2 0.000000 0.021488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018066 0.00000