HEADER REPLICATION 07-MAY-13 4BMD TITLE CRYSTAL STRUCTURE OF S.POMBE RAD4 BRCT3,4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-M CHECKPOINT CONTROL PROTEIN RAD4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BRCT3 AND BRCT4 DOMAINS, RESIDUES 291-494; COMPND 5 SYNONYM: RAD4, P74, PROTEIN CUT5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-28B KEYWDS REPLICATION, TOPBP1, BRCT, DNA DAMAGE CHECKPOINT EXPDTA X-RAY DIFFRACTION AUTHOR Q.MENG,M.RAPPAS,C.P.WARDLAW,V.GARCIA,A.M.CARR,A.W.OLIVER,L.L.DU, AUTHOR 2 L.H.PEARL REVDAT 2 20-DEC-23 4BMD 1 REMARK REVDAT 1 09-OCT-13 4BMD 0 JRNL AUTH M.QU,M.RAPPAS,C.P.WARDLAW,V.GARCIA,J.Y.REN,M.DAY,A.M.CARR, JRNL AUTH 2 A.W.OLIVER,L.L.DU,L.H.PEARL JRNL TITL PHOSPHORYLATION-DEPENDENT ASSEMBLY AND COORDINATION OF THE JRNL TITL 2 DNA DAMAGE CHECKPOINT APPARATUS BY RAD4(TOPBP1.). JRNL REF MOL.CELL V. 51 723 2013 JRNL REFN ISSN 1097-2765 JRNL PMID 24074952 JRNL DOI 10.1016/J.MOLCEL.2013.08.030 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.800 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 13109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1202 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 55.0612 - 5.1998 0.88 2327 132 0.1846 0.2098 REMARK 3 2 5.1998 - 4.1277 0.94 2502 140 0.1497 0.1655 REMARK 3 3 4.1277 - 3.6060 0.96 2535 143 0.1531 0.2069 REMARK 3 4 3.6060 - 3.2764 1.00 2683 114 0.1716 0.1875 REMARK 3 5 3.2764 - 3.0416 0.99 2650 147 0.1927 0.2615 REMARK 3 6 3.0416 - 2.8622 0.99 2648 112 0.2014 0.2557 REMARK 3 7 2.8622 - 2.7189 0.93 2519 121 0.2114 0.2558 REMARK 3 8 2.7189 - 2.6005 0.99 2626 134 0.2635 0.2901 REMARK 3 9 2.6005 - 2.5004 0.99 2635 159 0.3065 0.3282 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 57.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19900 REMARK 3 B22 (A**2) : 0.19900 REMARK 3 B33 (A**2) : -0.39800 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 : 0.002 1669 REMARK 3 ANGLE : 0.667 2285 REMARK 3 CHIRALITY : 0.043 248 REMARK 3 PLANARITY : 0.004 284 REMARK 3 DIHEDRAL : 9.301 617 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 4BMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9173 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13128 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 55.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.460 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.79 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 2XNH REMARK 200 REMARK 200 REMARK: BALBES SELECTED PDB ENTRY 2XNH AS THE BEST STARTING MODEL. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 0.2 M NACL, 20% PEG REMARK 280 6000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 25.13000 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 50.26000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.26000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.13000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 291 REMARK 465 THR A 292 REMARK 465 GLU A 293 REMARK 465 LEU A 294 REMARK 465 ASN A 295 REMARK 465 ILE A 296 REMARK 465 GLU A 297 REMARK 465 ASN A 298 REMARK 465 GLU A 299 REMARK 465 ALA A 300 REMARK 465 LYS A 489 REMARK 465 LYS A 490 REMARK 465 GLU A 491 REMARK 465 ASN A 492 REMARK 465 GLN A 493 REMARK 465 GLU A 494 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 LYS A 304 CG CD CE NZ REMARK 470 ARG A 462 CZ NH1 NH2 REMARK 470 ASP A 488 CG OD1 OD2 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 PHE A 303 36.07 -96.71 REMARK 500 SER A 358 30.74 -88.97 REMARK 500 SER A 358 31.30 -89.40 REMARK 500 GLN A 433 41.97 -97.88 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 CL A 1489 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 3001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BMC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S.POMBE RAD4 BRCT1,2 DBREF 4BMD A 291 494 UNP P32372 RAD4_SCHPO 291 494 SEQRES 1 A 204 ASP THR GLU LEU ASN ILE GLU ASN GLU ALA LYS LEU PHE SEQRES 2 A 204 LYS ASN LEU THR PHE TYR LEU TYR GLU PHE PRO ASN THR SEQRES 3 A 204 LYS VAL SER ARG LEU HIS LYS CYS LEU SER ASP ASN GLY SEQRES 4 A 204 GLY GLN ILE SER GLU PHE LEU SER SER THR ILE ASP PHE SEQRES 5 A 204 VAL VAL ILE PRO HIS TYR PHE PRO VAL ASP GLU LEU PRO SEQRES 6 A 204 ILE PHE SER PHE PRO THR VAL ASN GLU TRP TRP ILE GLU SEQRES 7 A 204 ARG CYS LEU TYR TYR LYS LYS ILE PHE GLY ILE ASP GLU SEQRES 8 A 204 HIS ALA LEU ALA LYS PRO PHE PHE ARG PRO SER LEU VAL SEQRES 9 A 204 PRO TYR PHE ASN GLY LEU SER ILE HIS LEU THR GLY PHE SEQRES 10 A 204 LYS GLY GLU GLU LEU SER HIS LEU LYS LYS ALA LEU THR SEQRES 11 A 204 ILE LEU GLY ALA VAL VAL HIS GLU PHE LEU GLY VAL GLN SEQRES 12 A 204 ARG SER ILE LEU LEU VAL ASN THR ASN GLU PRO PHE SER SEQRES 13 A 204 MET LYS THR ARG PHE LYS ILE GLN HIS ALA THR GLU TRP SEQRES 14 A 204 ASN VAL ARG VAL VAL GLY VAL ALA TRP LEU TRP ASN ILE SEQRES 15 A 204 ILE GLN SER GLY LYS PHE ILE ASP GLN VAL SER PRO TRP SEQRES 16 A 204 ALA ILE ASP LYS LYS GLU ASN GLN GLU HET CL A1489 1 HET MES A3001 12 HETNAM CL CHLORIDE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 CL CL 1- FORMUL 3 MES C6 H13 N O4 S FORMUL 4 HOH *144(H2 O) HELIX 1 1 PRO A 314 ASP A 327 1 14 HELIX 2 2 PRO A 350 LEU A 354 5 5 HELIX 3 3 GLU A 364 TYR A 373 1 10 HELIX 4 4 HIS A 382 LYS A 386 5 5 HELIX 5 5 ARG A 390 SER A 392 5 3 HELIX 6 6 LEU A 393 ASN A 398 1 6 HELIX 7 7 LYS A 408 LEU A 422 1 15 HELIX 8 8 SER A 446 TRP A 459 1 14 HELIX 9 9 VAL A 466 GLY A 476 1 11 HELIX 10 10 VAL A 482 TRP A 485 5 4 SHEET 1 AA 4 GLN A 331 ILE A 332 0 SHEET 2 AA 4 THR A 307 LEU A 310 1 N PHE A 308 O GLN A 331 SHEET 3 AA 4 PHE A 342 ILE A 345 1 O PHE A 342 N TYR A 309 SHEET 4 AA 4 THR A 361 ASN A 363 1 O VAL A 362 N ILE A 345 SHEET 1 AB 4 VAL A 425 HIS A 427 0 SHEET 2 AB 4 SER A 401 THR A 405 1 O ILE A 402 N HIS A 427 SHEET 3 AB 4 ILE A 436 VAL A 439 1 O ILE A 436 N HIS A 403 SHEET 4 AB 4 ARG A 462 GLY A 465 1 O ARG A 462 N LEU A 437 SITE 1 AC1 3 HIS A 427 PHE A 429 ARG A 434 SITE 1 AC2 8 GLU A 381 HIS A 382 ALA A 383 ARG A 434 SITE 2 AC2 8 ASN A 442 ALA A 467 TRP A 470 HOH A2135 CRYST1 93.030 93.030 75.390 90.00 90.00 120.00 P 31 2 1 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 0.010749 0.006206 0.000000 0.00000 SCALE2 0.000000 0.012412 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013264 0.00000