HEADER CELL CYCLE 12-SEP-18 6HM4 TITLE CRYSTAL STRUCTURE OF RAD4 BRCT1,2 IN COMPLEX WITH A MDB1 TITLE 2 PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-M CHECKPOINT CONTROL PROTEIN RAD4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P74,PROTEIN CUT5; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA DAMAGE RESPONSE PROTEIN MDB1; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: BRCT DOMAIN PROTEIN MDB1,MIDZONE AND DNA BREAK-LOCALIZING COMPND 10 PROTEIN 1; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC SOURCE 3 24843); SOURCE 4 ORGANISM_COMMON: FISSION YEAST; SOURCE 5 ORGANISM_TAXID: 284812; SOURCE 6 STRAIN: 972 / ATCC 24843; SOURCE 7 GENE: RAD4, CUT5, SPAC23C4.18C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 13 ORGANISM_COMMON: FISSION YEAST; SOURCE 14 ORGANISM_TAXID: 284812 KEYWDS BRCT DOMAIN PHOSPHOPEPTIDE RECOGNITION, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.DAY,M.RAPPAS,A.W.OLIVER,L.H.PEARL REVDAT 1 17-OCT-18 6HM4 0 JRNL AUTH M.DAY,M.RAPPAS,K.PTASINSKA,D.BOOS,A.W.OLIVER,L.H.PEARL JRNL TITL BRCT DOMAINS OF THE DNA DAMAGE CHECKPOINT PROTEINS JRNL TITL 2 TOPBP1/RAD4 DISPLAY DISTINCT SPECIFICITIES FOR JRNL TITL 3 PHOSPHOPEPTIDE LIGANDS. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 30295604 JRNL DOI 10.7554/ELIFE.39979 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.365 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 19338 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.125 REMARK 3 FREE R VALUE TEST SET COUNT : 991 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 31.9431 - 3.3851 0.96 2761 144 0.1520 0.1775 REMARK 3 2 3.3851 - 2.6873 0.97 2754 145 0.1585 0.1968 REMARK 3 3 2.6873 - 2.3477 0.98 2775 139 0.1651 0.2151 REMARK 3 4 2.3477 - 2.1331 0.98 2744 156 0.1607 0.2275 REMARK 3 5 2.1331 - 1.9802 0.98 2748 139 0.1738 0.2385 REMARK 3 6 1.9802 - 1.8635 0.92 2555 140 0.2093 0.2560 REMARK 3 7 1.8635 - 1.7702 0.72 2010 128 0.2752 0.3554 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) : 0.232 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.572 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.63 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 : 0.006 1595 REMARK 3 ANGLE : 0.833 2167 REMARK 3 CHIRALITY : 0.052 242 REMARK 3 PLANARITY : 0.005 272 REMARK 3 DIHEDRAL : 4.707 1299 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 6HM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-14 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19339 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 31.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM ACETATE TRIHYDRATE, 100 REMARK 280 MM TRIS 8.5 AND 30 % W/V PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 287.15K 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 20.00000 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: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 GLN B 115 REMARK 465 LYS B 116 REMARK 465 PRO B 117 REMARK 465 ASN B 118 REMARK 465 LEU B 119 REMARK 465 GLN B 120 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 5 CG CD CE NZ REMARK 470 LYS A 20 CG CD CE NZ 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 O HOH A 415 O HOH A 479 1.81 REMARK 500 O HOH A 320 O HOH A 496 1.91 REMARK 500 NZ LYS A 104 O HOH A 301 1.95 REMARK 500 O HOH A 526 O HOH A 546 1.96 REMARK 500 N LYS A 5 O HOH A 302 2.01 REMARK 500 OE1 GLU A 73 O HOH A 303 2.08 REMARK 500 O HOH A 553 O HOH A 560 2.09 REMARK 500 O HOH A 439 O HOH A 466 2.10 REMARK 500 O HOH A 522 O HOH A 524 2.10 REMARK 500 O HOH A 407 O HOH A 525 2.11 REMARK 500 O HOH A 469 O HOH A 472 2.13 REMARK 500 O HOH A 413 O HOH A 448 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 514 O HOH A 539 1455 2.11 REMARK 500 O HOH A 382 O HOH A 408 2445 2.12 REMARK 500 O HOH A 441 O HOH A 466 1455 2.13 REMARK 500 O HOH A 331 O HOH A 371 2444 2.16 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 ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 DBREF 6HM4 A 1 186 UNP P32372 RAD4_SCHPO 1 186 DBREF 6HM4 B 106 120 UNP O14079 MDB1_SCHPO 106 120 SEQRES 1 A 186 MET GLY SER SER LYS PRO LEU LYS GLY PHE VAL ILE CYS SEQRES 2 A 186 CYS THR SER ILE ASP LEU LYS GLN ARG THR GLU ILE SER SEQRES 3 A 186 THR LYS ALA THR LYS LEU GLY ALA ALA TYR ARG SER ASP SEQRES 4 A 186 PHE THR LYS ASP VAL THR HIS LEU ILE ALA GLY ASP PHE SEQRES 5 A 186 ASP THR PRO LYS TYR LYS PHE ALA ALA LYS SER ARG PRO SEQRES 6 A 186 ASP ILE LYS ILE MET SER SER GLU TRP ILE PRO VAL LEU SEQRES 7 A 186 TYR GLU SER TRP VAL GLN GLY GLU ASP LEU ASP ASP GLY SEQRES 8 A 186 LEU LEU VAL ASP LYS HIS PHE LEU PRO THR LEU PHE LYS SEQRES 9 A 186 CYS ARG VAL CYS LEU THR ASN ILE GLY GLN PRO GLU ARG SEQRES 10 A 186 SER ARG ILE GLU ASN TYR VAL LEU LYS HIS GLY GLY THR SEQRES 11 A 186 PHE CYS PRO ASP LEU THR ARG ASP VAL THR HIS LEU ILE SEQRES 12 A 186 ALA GLY THR SER SER GLY ARG LYS TYR GLU TYR ALA LEU SEQRES 13 A 186 LYS TRP LYS ILE ASN VAL VAL CSO VAL GLU TRP LEU TRP SEQRES 14 A 186 GLN SER ILE GLN ARG ASN ALA VAL LEU GLU PRO GLN TYR SEQRES 15 A 186 PHE GLN LEU ASP SEQRES 1 B 15 GLY VAL MET THR VAL PRO ASN TPO PRO GLN LYS PRO ASN SEQRES 2 B 15 LEU GLN MODRES 6HM4 CSO A 164 CYS MODIFIED RESIDUE MODRES 6HM4 TPO B 113 THR MODIFIED RESIDUE HET CSO A 164 7 HET TPO B 113 11 HET ACT A 201 4 HET EDO A 202 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM TPO PHOSPHOTHREONINE HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN TPO PHOSPHONOTHREONINE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 TPO C4 H10 N O6 P FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *288(H2 O) HELIX 1 AA1 ASP A 18 LEU A 32 1 15 HELIX 2 AA2 THR A 54 ARG A 64 1 11 HELIX 3 AA3 GLU A 73 GLN A 84 1 12 HELIX 4 AA4 LEU A 93 HIS A 97 5 5 HELIX 5 AA5 PRO A 115 HIS A 127 1 13 HELIX 6 AA6 GLY A 149 TRP A 158 1 10 HELIX 7 AA7 VAL A 165 ASN A 175 1 11 HELIX 8 AA8 GLU A 179 GLN A 184 5 6 SHEET 1 AA1 4 ALA A 35 ARG A 37 0 SHEET 2 AA1 4 VAL A 11 THR A 15 1 N ILE A 12 O ALA A 35 SHEET 3 AA1 4 HIS A 46 ALA A 49 1 O ILE A 48 N CYS A 13 SHEET 4 AA1 4 LYS A 68 MET A 70 1 O MET A 70 N LEU A 47 SHEET 1 AA2 4 THR A 130 PHE A 131 0 SHEET 2 AA2 4 ARG A 106 THR A 110 1 N VAL A 107 O THR A 130 SHEET 3 AA2 4 HIS A 141 ALA A 144 1 O ILE A 143 N CYS A 108 SHEET 4 AA2 4 ASN A 161 VAL A 163 1 O ASN A 161 N LEU A 142 LINK C VAL A 163 N CSO A 164 1555 1555 1.32 LINK C CSO A 164 N VAL A 165 1555 1555 1.33 LINK C ASN B 112 N TPO B 113 1555 1555 1.33 LINK C TPO B 113 N PRO B 114 1555 1555 1.34 CISPEP 1 GLN A 114 PRO A 115 0 0.59 SITE 1 AC1 6 ALA A 49 GLY A 50 SER A 71 SER A 72 SITE 2 AC1 6 LEU A 99 PHE A 103 SITE 1 AC2 3 ASP A 51 LYS A 104 HOH A 318 CRYST1 50.170 40.000 54.960 90.00 105.16 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 0.019932 0.000000 0.005401 0.00000 SCALE2 0.000000 0.025000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018851 0.00000