HEADER TRANSCRIPTION 13-AUG-16 5LPJ TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN CREBBP BOUND TO THE TITLE 2 INHIBITOR XDM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN, 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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS BROMODOMAIN, PROTEIN-INHIBITOR COMPLEX, EPIGENETICS, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.HUEGLE,D.WOHLWEND REVDAT 3 01-MAY-24 5LPJ 1 REMARK REVDAT 2 11-OCT-17 5LPJ 1 JRNL REVDAT 1 16-AUG-17 5LPJ 0 JRNL AUTH M.HUGLE,X.LUCAS,D.OSTROVSKYI,P.REGENASS,S.GERHARDT,O.EINSLE, JRNL AUTH 2 M.HAU,M.JUNG,B.BREIT,S.GUNTHER,D.WOHLWEND JRNL TITL BEYOND THE BET FAMILY: TARGETING CBP/P300 WITH 4-ACYL JRNL TITL 2 PYRROLES. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 56 12476 2017 JRNL REFN ESSN 1521-3773 JRNL PMID 28766825 JRNL DOI 10.1002/ANIE.201705516 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1694 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 42.0550 - 3.7769 1.00 1385 150 0.1443 0.1663 REMARK 3 2 3.7769 - 2.9981 1.00 1309 156 0.1526 0.1725 REMARK 3 3 2.9981 - 2.6192 1.00 1280 154 0.1694 0.2156 REMARK 3 4 2.6192 - 2.3797 1.00 1275 139 0.1618 0.2009 REMARK 3 5 2.3797 - 2.2092 1.00 1278 152 0.1596 0.1770 REMARK 3 6 2.2092 - 2.0789 1.00 1267 132 0.1510 0.1944 REMARK 3 7 2.0789 - 1.9748 1.00 1247 145 0.1646 0.1989 REMARK 3 8 1.9748 - 1.8888 1.00 1261 129 0.1894 0.2268 REMARK 3 9 1.8888 - 1.8161 1.00 1276 128 0.2084 0.2302 REMARK 3 10 1.8161 - 1.7535 1.00 1242 144 0.2209 0.2495 REMARK 3 11 1.7535 - 1.6986 1.00 1266 123 0.2537 0.2727 REMARK 3 12 1.6986 - 1.6501 1.00 1239 142 0.2742 0.3227 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.74 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 : 0.003 1088 REMARK 3 ANGLE : 0.692 1496 REMARK 3 CHIRALITY : 0.042 154 REMARK 3 PLANARITY : 0.005 212 REMARK 3 DIHEDRAL : 15.759 689 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): -21.9409 52.1717 6.9019 REMARK 3 T TENSOR REMARK 3 T11: 0.1502 T22: 0.0990 REMARK 3 T33: 0.1052 T12: 0.0139 REMARK 3 T13: 0.0211 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.6965 L22: 1.6472 REMARK 3 L33: 2.9616 L12: 0.1066 REMARK 3 L13: 0.8072 L23: -0.2250 REMARK 3 S TENSOR REMARK 3 S11: 0.0627 S12: -0.0461 S13: -0.0852 REMARK 3 S21: 0.0675 S22: 0.0094 S23: -0.0026 REMARK 3 S31: 0.2852 S32: 0.0029 S33: -0.0665 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 5LPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : FIXED-EXIT LN2 COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 49.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.26800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 20.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 0.78800 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: PHASER 2.6.0 REMARK 200 STARTING MODEL: APO-CBP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LISO4, PEG 3350, PH 6.5, EVAPORATION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 17.10800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.36500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.62300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.36500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.10800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.62300 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 SER A 1079 REMARK 465 MET A 1080 REMARK 465 ARG A 1081 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 A1082 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 OD1 ASP A 1190 O HOH A 1301 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1508 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A1509 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A1510 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A1511 DISTANCE = 7.95 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XDM A 1201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NRW RELATED DB: PDB DBREF 5LPJ A 1081 1197 UNP Q92793 CBP_HUMAN 1081 1197 SEQADV 5LPJ SER A 1079 UNP Q92793 EXPRESSION TAG SEQADV 5LPJ MET A 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 HET XDM A1201 41 HETNAM XDM ~{N}-[(3-CHLOROPHENYL)METHYL]-4-ETHANOYL-3-ETHYL-5- HETNAM 2 XDM METHYL-1~{H}-PYRROLE-2-CARBOXAMIDE HETSYN XDM XDM1 FORMUL 2 XDM C17 H19 CL N2 O2 FORMUL 3 HOH *211(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 1124 VAL A 1129 1 6 HELIX 4 AA4 ASP A 1134 THR A 1144 1 11 HELIX 5 AA5 GLU A 1149 ASN A 1168 1 20 HELIX 6 AA6 SER A 1172 LEU A 1196 1 25 CISPEP 1 ASP A 1105 PRO A 1106 0 10.23 SITE 1 AC1 14 PRO A1110 VAL A1115 LEU A1120 ILE A1122 SITE 2 AC1 14 TYR A1125 TYR A1167 ASN A1168 ARG A1173 SITE 3 AC1 14 VAL A1174 PHE A1177 HOH A1325 HOH A1384 SITE 4 AC1 14 HOH A1413 HOH A1426 CRYST1 34.216 49.246 80.730 90.00 90.00 90.00 P 21 21 21 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 0.029226 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020306 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012387 0.00000