HEADER TRANSFERASE/TRANSFERASE INHIBITOR 23-SEP-14 4WHU TITLE BROMO DOMAIN OF CREB BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1081-1197; COMPND 5 EC: 2.3.1.48; 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: CREBBP, CBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS BROMO DOMAIN, CREB BINDING PROTEIN, INHIBITOR, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU REVDAT 2 27-SEP-23 4WHU 1 REMARK REVDAT 1 28-OCT-15 4WHU 0 JRNL AUTH E.C.HETT,E.L.PIATNITSKI CHEKLER,A.BASAK,P.D.BONIN,R.A.DENNY, JRNL AUTH 2 A.C.FLICK,K.F.GEOGHEGAN,S.LIU,M.T.PLETCHER,R.P.ROBINSON, JRNL AUTH 3 P.SAHASRABUDHE,S.SALTER,I.A.STOCK,L.H.JONES JRNL TITL DIRECT PHOTOCAPTURE OF BROMODOMAINS USING TROPOLONE CHEMICAL JRNL TITL 2 PROBES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 6341 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.560 REMARK 3 FREE R VALUE TEST SET COUNT : 289 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.69 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1737 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2263 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1657 REMARK 3 BIN R VALUE (WORKING SET) : 0.2239 REMARK 3 BIN FREE R VALUE : 0.2813 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.61 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 80 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 : 988 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.01970 REMARK 3 B22 (A**2) : 2.17610 REMARK 3 B33 (A**2) : -5.19580 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.67080 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.430 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.288 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.217 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.311 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.223 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1087 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1504 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 378 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 30 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 183 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1087 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 124 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1181 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.95 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.06 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.18 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 5.1600 39.0207 10.1890 REMARK 3 T TENSOR REMARK 3 T11: 0.1312 T22: -0.0181 REMARK 3 T33: -0.0599 T12: 0.1323 REMARK 3 T13: -0.0054 T23: -0.0350 REMARK 3 L TENSOR REMARK 3 L11: 4.9017 L22: 7.3293 REMARK 3 L33: 5.6448 L12: -2.2277 REMARK 3 L13: 0.4999 L23: 0.4128 REMARK 3 S TENSOR REMARK 3 S11: -0.5648 S12: -0.6987 S13: -0.0750 REMARK 3 S21: 1.1820 S22: 0.2642 S23: 0.1650 REMARK 3 S31: -0.5963 S32: -0.5230 S33: 0.3006 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4WHU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 32.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3DVW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: OBTAINED THROUGH SCREEN WITH HAMPTON REMARK 280 RESEARCH KITS (HT AND INDEX), VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 21.65850 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: 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 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 ARG A1081 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1082 NZ REMARK 470 LYS A1170 CD CE NZ REMARK 470 GLN A1187 CD OE1 NE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3OT A 4000 DBREF 4WHU A 1081 1197 UNP Q92793 CBP_HUMAN 1081 1197 SEQADV 4WHU SER A 1079 UNP Q92793 EXPRESSION TAG SEQADV 4WHU MET A 1080 UNP Q92793 INITIATING METHIONINE 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 HET 3OT A4000 66 HETNAM 3OT 2-METHOXY-4-{1-[2-(MORPHOLIN-4-YL)ETHYL]-2-(2- HETNAM 2 3OT PHENYLETHYL)-1H-BENZIMIDAZOL-5-YL}CYCLOHEPTA-2,4,6- HETNAM 3 3OT TRIEN-1-ONE FORMUL 2 3OT C29 H31 N3 O3 FORMUL 3 HOH *13(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 GLY A 1145 1 12 HELIX 6 AA6 GLU A 1149 ASN A 1168 1 20 HELIX 7 AA7 SER A 1172 GLY A 1197 1 26 CISPEP 1 ASP A 1105 PRO A 1106 0 5.24 SITE 1 AC1 12 LEU A1109 PRO A1110 PHE A1111 VAL A1115 SITE 2 AC1 12 LEU A1119 LEU A1120 TYR A1125 ASN A1168 SITE 3 AC1 12 ARG A1173 VAL A1174 PHE A1177 HOH A4109 CRYST1 25.284 43.317 51.387 90.00 98.68 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 0.039551 0.000000 0.006038 0.00000 SCALE2 0.000000 0.023086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019686 0.00000