HEADER TRANSFERASE 14-FEB-18 6FQO TITLE CRYSTAL STRUCTURE OF CREBBP BROMODOMAIN COMPLEXD WITH DT29 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.3.1.48; COMPND 5 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: CREBBP, CBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INHIBITOR, BROMODOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHU,A.CAFLISCH REVDAT 3 17-JAN-24 6FQO 1 REMARK REVDAT 2 10-OCT-18 6FQO 1 JRNL REVDAT 1 29-AUG-18 6FQO 0 JRNL AUTH J.ZHU,J.DONG,L.BATISTE,A.UNZUE,A.DOLBOIS,V.PASCANU,P.SLEDZ, JRNL AUTH 2 C.NEVADO,A.CAFLISCH JRNL TITL BINDING MOTIFS IN THE CBP BROMODOMAIN: AN ANALYSIS OF 20 JRNL TITL 2 CRYSTAL STRUCTURES OF COMPLEXES WITH SMALL MOLECULES. JRNL REF ACS MED CHEM LETT V. 9 929 2018 JRNL REFN ISSN 1948-5875 JRNL PMID 30258543 JRNL DOI 10.1021/ACSMEDCHEMLETT.8B00286 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 48329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 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 38.9286 - 3.2531 0.99 3428 151 0.1685 0.1912 REMARK 3 2 3.2531 - 2.5823 1.00 3363 148 0.1754 0.1838 REMARK 3 3 2.5823 - 2.2559 1.00 3372 143 0.1703 0.1875 REMARK 3 4 2.2559 - 2.0496 1.00 3329 149 0.1567 0.1824 REMARK 3 5 2.0496 - 1.9027 1.00 3332 145 0.1689 0.1924 REMARK 3 6 1.9027 - 1.7906 1.00 3363 142 0.1724 0.2099 REMARK 3 7 1.7906 - 1.7009 1.00 3328 144 0.1655 0.1933 REMARK 3 8 1.7009 - 1.6268 1.00 3317 145 0.1630 0.2003 REMARK 3 9 1.6268 - 1.5642 1.00 3312 140 0.1610 0.1964 REMARK 3 10 1.5642 - 1.5102 0.99 3275 140 0.1681 0.1953 REMARK 3 11 1.5102 - 1.4630 0.98 3255 139 0.1714 0.1975 REMARK 3 12 1.4630 - 1.4212 0.97 3259 144 0.1973 0.2246 REMARK 3 13 1.4212 - 1.3838 0.97 3210 135 0.2040 0.2208 REMARK 3 14 1.3838 - 1.3500 0.96 3184 137 0.2208 0.2775 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2113 REMARK 3 ANGLE : 1.126 2877 REMARK 3 CHIRALITY : 0.074 290 REMARK 3 PLANARITY : 0.007 374 REMARK 3 DIHEDRAL : 11.636 1335 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.1606 0.5657 16.5162 REMARK 3 T TENSOR REMARK 3 T11: 0.1005 T22: 0.0844 REMARK 3 T33: 0.0691 T12: -0.0063 REMARK 3 T13: -0.0012 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.1570 L22: 0.4600 REMARK 3 L33: 0.3240 L12: 0.1901 REMARK 3 L13: -0.0902 L23: -0.1122 REMARK 3 S TENSOR REMARK 3 S11: -0.0258 S12: 0.1348 S13: 0.0230 REMARK 3 S21: -0.0588 S22: 0.0250 S23: -0.0070 REMARK 3 S31: 0.0017 S32: 0.0103 S33: 0.0024 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 6FQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-17 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999989 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48359 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 43.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.45200 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: MOLREP REMARK 200 STARTING MODEL: 3DWY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M KSCN, 20% PEG3350, 10% EG, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 21.83200 REMARK 290 SMTRY3 2 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 SER A 1079 REMARK 465 MET A 1080 REMARK 465 ARG A 1081 REMARK 465 LYS A 1082 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 A1186 CD OE1 OE2 REMARK 470 GLN A1187 CG CD OE1 NE2 REMARK 470 GLY A1197 C O REMARK 470 GLU B1089 CG CD OE1 OE2 REMARK 470 GLN B1092 CG CD OE1 NE2 REMARK 470 GLN B1187 CG CD OE1 NE2 REMARK 470 GLN B1194 CG CD OE1 NE2 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 OD1 ASN A 1131 O HOH A 1301 2.14 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 E2T A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue E2T B 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 1202 DBREF 6FQO A 1081 1197 UNP Q92793 CBP_HUMAN 1081 1197 DBREF 6FQO B 1081 1197 UNP Q92793 CBP_HUMAN 1081 1197 SEQADV 6FQO SER A 1079 UNP Q92793 EXPRESSION TAG SEQADV 6FQO MET A 1080 UNP Q92793 EXPRESSION TAG SEQADV 6FQO SER B 1079 UNP Q92793 EXPRESSION TAG SEQADV 6FQO MET B 1080 UNP Q92793 EXPRESSION TAG SEQRES 1 A 119 SER MET ARG LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG SEQRES 2 A 119 GLN ALA LEU MET PRO THR LEU GLU ALA LEU TYR ARG GLN SEQRES 3 A 119 ASP PRO GLU SER LEU PRO PHE ARG GLN PRO VAL ASP PRO SEQRES 4 A 119 GLN LEU LEU GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS SEQRES 5 A 119 ASN PRO MET ASP LEU SER THR ILE LYS ARG LYS LEU ASP SEQRES 6 A 119 THR GLY GLN TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP SEQRES 7 A 119 VAL TRP LEU MET PHE ASN ASN ALA TRP LEU TYR ASN ARG SEQRES 8 A 119 LYS THR SER ARG VAL TYR LYS PHE CYS SER LYS LEU ALA SEQRES 9 A 119 GLU VAL PHE GLU GLN GLU ILE ASP PRO VAL MET GLN SER SEQRES 10 A 119 LEU GLY SEQRES 1 B 119 SER MET ARG LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG SEQRES 2 B 119 GLN ALA LEU MET PRO THR LEU GLU ALA LEU TYR ARG GLN SEQRES 3 B 119 ASP PRO GLU SER LEU PRO PHE ARG GLN PRO VAL ASP PRO SEQRES 4 B 119 GLN LEU LEU GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS SEQRES 5 B 119 ASN PRO MET ASP LEU SER THR ILE LYS ARG LYS LEU ASP SEQRES 6 B 119 THR GLY GLN TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP SEQRES 7 B 119 VAL TRP LEU MET PHE ASN ASN ALA TRP LEU TYR ASN ARG SEQRES 8 B 119 LYS THR SER ARG VAL TYR LYS PHE CYS SER LYS LEU ALA SEQRES 9 B 119 GLU VAL PHE GLU GLN GLU ILE ASP PRO VAL MET GLN SER SEQRES 10 B 119 LEU GLY HET E2T A1201 34 HET EDO A1202 4 HET E2T B1201 34 HET EDO B1202 4 HETNAM E2T ~{N}-[3-(2,5-DIMETHYL-3-OXIDANYLIDENE-1,2-OXAZOL-4-YL)- HETNAM 2 E2T 5-(5-ETHANOYL-2-ETHOXY-PHENYL)PHENYL]FURAN-2- HETNAM 3 E2T CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 E2T 2(C26 H24 N2 O6) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 HOH *285(H2 O) HELIX 1 AA1 LYS A 1086 ARG A 1103 1 18 HELIX 2 AA2 SER A 1108 ARG A 1112 5 5 HELIX 3 AA3 ASP A 1116 GLY A 1121 1 6 HELIX 4 AA4 ASP A 1124 VAL A 1129 1 6 HELIX 5 AA5 ASP A 1134 THR A 1144 1 11 HELIX 6 AA6 GLU A 1149 ASN A 1168 1 20 HELIX 7 AA7 SER A 1172 LEU A 1196 1 25 HELIX 8 AA8 LYS B 1086 GLN B 1104 1 19 HELIX 9 AA9 SER B 1108 ARG B 1112 5 5 HELIX 10 AB1 ASP B 1116 GLY B 1121 1 6 HELIX 11 AB2 ASP B 1124 VAL B 1129 1 6 HELIX 12 AB3 ASP B 1134 THR B 1144 1 11 HELIX 13 AB4 GLU B 1149 ASN B 1168 1 20 HELIX 14 AB5 SER B 1172 GLY B 1197 1 26 CISPEP 1 ASP A 1105 PRO A 1106 0 10.38 CISPEP 2 ASP B 1105 PRO B 1106 0 12.04 SITE 1 AC1 14 LEU A1109 PRO A1110 GLN A1113 VAL A1115 SITE 2 AC1 14 LEU A1120 ILE A1122 ASN A1168 ARG A1173 SITE 3 AC1 14 EDO A1202 HOH A1309 HOH A1330 HOH A1371 SITE 4 AC1 14 HOH A1445 TRP B1165 SITE 1 AC2 7 GLN A1113 PRO A1114 E2T A1201 HOH A1352 SITE 2 AC2 7 HOH A1378 ASN B1162 TRP B1165 SITE 1 AC3 11 HOH A1431 LEU B1109 PRO B1110 GLN B1113 SITE 2 AC3 11 VAL B1115 LEU B1120 ASN B1168 ARG B1173 SITE 3 AC3 11 HOH B1309 HOH B1310 HOH B1380 SITE 1 AC4 5 LEU B1159 ASN B1162 ASN B1163 HOH B1339 SITE 2 AC4 5 HOH B1368 CRYST1 50.736 43.664 51.301 90.00 99.42 90.00 P 1 21 1 4 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 0.019710 0.000000 0.003268 0.00000 SCALE2 0.000000 0.022902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019759 0.00000