HEADER CELL CYCLE 20-JUL-05 2ADO TITLE CRYSTAL STRUCTURE OF THE BRCT REPEAT REGION FROM THE MEDIATOR OF DNA TITLE 2 DAMAGE CHECKPOINT PROTEIN 1, MDC1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEDIATOR OF DNA DAMAGE CHECKPOINT PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1891-2086; COMPND 5 SYNONYM: NUCLEAR FACTOR WITH BRCT DOMAINS 1; 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 GENE: MDC1, KIAA0170, NFBD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GOLD99; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PDEST15 KEYWDS BRCT REPEATS, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.LEE,R.A.EDWARDS,G.L.THEDE,J.N.GLOVER REVDAT 5 14-FEB-24 2ADO 1 REMARK REVDAT 4 11-OCT-17 2ADO 1 REMARK REVDAT 3 24-FEB-09 2ADO 1 VERSN REVDAT 2 27-SEP-05 2ADO 1 JRNL REVDAT 1 02-AUG-05 2ADO 0 JRNL AUTH M.S.LEE,R.A.EDWARDS,G.L.THEDE,J.N.GLOVER JRNL TITL STRUCTURE OF THE BRCT REPEAT DOMAIN OF MDC1 AND ITS JRNL TITL 2 SPECIFICITY FOR THE FREE COOH-TERMINAL END OF THE JRNL TITL 3 {GAMMA}-H2AX HISTONE TAIL. JRNL REF J.BIOL.CHEM. V. 280 32053 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 16049003 JRNL DOI 10.1074/JBC.C500273200 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 60499 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2991 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2999 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.66900 REMARK 3 B22 (A**2) : 0.79600 REMARK 3 B33 (A**2) : -1.46500 REMARK 3 B12 (A**2) : 0.13100 REMARK 3 B13 (A**2) : -0.44400 REMARK 3 B23 (A**2) : 0.87600 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL 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 : NULL REMARK 3 BSOL : 47.05 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ADO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1159,0.9795471,1.019876 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 2.08, RESOLVE 2.08 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, HEPES, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K. SODIUM DIHYDROGEN REMARK 280 ORTHOPHOSPHATE, POTASSIUM PHOSPHATE DIBASIC, SODIUM CITRATE, PH REMARK 280 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 THR A 1891 REMARK 465 MET A 2086 REMARK 465 MET B 2086 DBREF 2ADO A 1891 2086 UNP Q14676 MDC1_HUMAN 1891 2086 DBREF 2ADO B 1891 2086 UNP Q14676 MDC1_HUMAN 1891 2086 SEQRES 1 A 196 THR ALA PRO LYS VAL LEU PHE THR GLY VAL VAL ASP ALA SEQRES 2 A 196 ARG GLY GLU ARG ALA VAL LEU ALA LEU GLY GLY SER LEU SEQRES 3 A 196 ALA GLY SER ALA ALA GLU ALA SER HIS LEU VAL THR ASP SEQRES 4 A 196 ARG ILE ARG ARG THR VAL LYS PHE LEU CYS ALA LEU GLY SEQRES 5 A 196 ARG GLY ILE PRO ILE LEU SER LEU ASP TRP LEU HIS GLN SEQRES 6 A 196 SER ARG LYS ALA GLY PHE PHE LEU PRO PRO ASP GLU TYR SEQRES 7 A 196 VAL VAL THR ASP PRO GLU GLN GLU LYS ASN PHE GLY PHE SEQRES 8 A 196 SER LEU GLN ASP ALA LEU SER ARG ALA ARG GLU ARG ARG SEQRES 9 A 196 LEU LEU GLU GLY TYR GLU ILE TYR VAL THR PRO GLY VAL SEQRES 10 A 196 GLN PRO PRO PRO PRO GLN MET GLY GLU ILE ILE SER CYS SEQRES 11 A 196 CYS GLY GLY THR TYR LEU PRO SER MET PRO ARG SER TYR SEQRES 12 A 196 LYS PRO GLN ARG VAL VAL ILE THR CYS PRO GLN ASP PHE SEQRES 13 A 196 PRO HIS CYS SER ILE PRO LEU ARG VAL GLY LEU PRO LEU SEQRES 14 A 196 LEU SER PRO GLU PHE LEU LEU THR GLY VAL LEU LYS GLN SEQRES 15 A 196 GLU ALA LYS PRO GLU ALA PHE VAL LEU SER PRO LEU GLU SEQRES 16 A 196 MET SEQRES 1 B 196 THR ALA PRO LYS VAL LEU PHE THR GLY VAL VAL ASP ALA SEQRES 2 B 196 ARG GLY GLU ARG ALA VAL LEU ALA LEU GLY GLY SER LEU SEQRES 3 B 196 ALA GLY SER ALA ALA GLU ALA SER HIS LEU VAL THR ASP SEQRES 4 B 196 ARG ILE ARG ARG THR VAL LYS PHE LEU CYS ALA LEU GLY SEQRES 5 B 196 ARG GLY ILE PRO ILE LEU SER LEU ASP TRP LEU HIS GLN SEQRES 6 B 196 SER ARG LYS ALA GLY PHE PHE LEU PRO PRO ASP GLU TYR SEQRES 7 B 196 VAL VAL THR ASP PRO GLU GLN GLU LYS ASN PHE GLY PHE SEQRES 8 B 196 SER LEU GLN ASP ALA LEU SER ARG ALA ARG GLU ARG ARG SEQRES 9 B 196 LEU LEU GLU GLY TYR GLU ILE TYR VAL THR PRO GLY VAL SEQRES 10 B 196 GLN PRO PRO PRO PRO GLN MET GLY GLU ILE ILE SER CYS SEQRES 11 B 196 CYS GLY GLY THR TYR LEU PRO SER MET PRO ARG SER TYR SEQRES 12 B 196 LYS PRO GLN ARG VAL VAL ILE THR CYS PRO GLN ASP PHE SEQRES 13 B 196 PRO HIS CYS SER ILE PRO LEU ARG VAL GLY LEU PRO LEU SEQRES 14 B 196 LEU SER PRO GLU PHE LEU LEU THR GLY VAL LEU LYS GLN SEQRES 15 B 196 GLU ALA LYS PRO GLU ALA PHE VAL LEU SER PRO LEU GLU SEQRES 16 B 196 MET FORMUL 3 HOH *256(H2 O) HELIX 1 1 ASP A 1902 LEU A 1912 1 11 HELIX 2 2 THR A 1934 GLY A 1944 1 11 HELIX 3 3 LEU A 1950 GLY A 1960 1 11 HELIX 4 4 PRO A 1965 VAL A 1969 5 5 HELIX 5 5 ASP A 1972 GLY A 1980 1 9 HELIX 6 6 SER A 1982 ARG A 1993 1 12 HELIX 7 7 PRO A 2010 CYS A 2021 1 12 HELIX 8 8 CYS A 2042 HIS A 2048 5 7 HELIX 9 9 CYS A 2049 GLY A 2056 1 8 HELIX 10 10 SER A 2061 GLN A 2072 1 12 HELIX 11 11 LYS A 2075 PHE A 2079 5 5 HELIX 12 12 ASP B 1902 LEU B 1912 1 11 HELIX 13 13 THR B 1934 GLY B 1944 1 11 HELIX 14 14 LEU B 1950 GLY B 1960 1 11 HELIX 15 15 PRO B 1965 VAL B 1969 5 5 HELIX 16 16 ASP B 1972 GLY B 1980 1 9 HELIX 17 17 SER B 1982 ARG B 1993 1 12 HELIX 18 18 PRO B 2010 CYS B 2021 1 12 HELIX 19 19 CYS B 2042 HIS B 2048 5 7 HELIX 20 20 CYS B 2049 GLY B 2056 1 8 HELIX 21 21 SER B 2061 GLN B 2072 1 12 HELIX 22 22 LYS B 2075 VAL B 2080 5 6 SHEET 1 A 4 SER A1915 LEU A1916 0 SHEET 2 A 4 LYS A1894 PHE A1897 1 N VAL A1895 O SER A1915 SHEET 3 A 4 HIS A1925 VAL A1927 1 O VAL A1927 N LEU A1896 SHEET 4 A 4 ILE A1947 LEU A1948 1 O LEU A1948 N LEU A1926 SHEET 1 B 4 THR A2024 TYR A2025 0 SHEET 2 B 4 GLU A2000 VAL A2003 1 N ILE A2001 O THR A2024 SHEET 3 B 4 ARG A2037 ILE A2040 1 O ILE A2040 N TYR A2002 SHEET 4 B 4 LEU A2059 LEU A2060 1 O LEU A2060 N VAL A2039 SHEET 1 C 4 SER B1915 LEU B1916 0 SHEET 2 C 4 LYS B1894 PHE B1897 1 N VAL B1895 O SER B1915 SHEET 3 C 4 HIS B1925 VAL B1927 1 O VAL B1927 N LEU B1896 SHEET 4 C 4 ILE B1947 LEU B1948 1 O LEU B1948 N LEU B1926 SHEET 1 D 4 THR B2024 TYR B2025 0 SHEET 2 D 4 GLU B2000 VAL B2003 1 N ILE B2001 O THR B2024 SHEET 3 D 4 ARG B2037 ILE B2040 1 O ILE B2040 N TYR B2002 SHEET 4 D 4 LEU B2059 LEU B2060 1 O LEU B2060 N VAL B2039 CISPEP 1 GLN A 2008 PRO A 2009 0 0.46 CISPEP 2 GLN B 2008 PRO B 2009 0 0.13 CRYST1 42.051 44.440 61.942 72.95 87.54 61.80 P 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 0.023781 -0.012751 0.003083 0.00000 SCALE2 0.000000 0.025533 -0.008324 0.00000 SCALE3 0.000000 0.000000 0.016996 0.00000