HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 04-DEC-15 5F5Z
TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX
TITLE 2 WITH MA2-014
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 44-168;
COMPND 5 SYNONYM: PROTEIN HUNK1;
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: BRD4, HUNK1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4
KEYWDS BROMODOMAIN, CAP, HUNK1, MCAP, PROTEIN BINDING-INHIBITOR COMPLEX,
KEYWDS 2 MITOTIC CHROMOSOME ASSOCIATED PROTEIN, CELL CYCLE, INHIBITOR,
KEYWDS 3 TRANSCRIPTION-INHIBITOR COMPLEX, TRANSCRIPTION-TRANSCRIPTION
KEYWDS 4 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.W.EMBER,J.-Y.ZHU,E.SCHONBRUNN
REVDAT 3 27-SEP-23 5F5Z 1 REMARK
REVDAT 2 14-JUN-17 5F5Z 1 JRNL
REVDAT 1 05-APR-17 5F5Z 0
JRNL AUTH S.W.EMBER,Q.T.LAMBERT,N.BERNDT,S.GUNAWAN,M.AYAZ,M.TAURO,
JRNL AUTH 2 J.Y.ZHU,P.J.CRANFILL,P.GRENINGER,C.C.LYNCH,C.H.BENES,
JRNL AUTH 3 H.R.LAWRENCE,G.W.REUTHER,N.J.LAWRENCE,E.SCHONBRUNN
JRNL TITL POTENT DUAL BET BROMODOMAIN-KINASE INHIBITORS AS VALUE-ADDED
JRNL TITL 2 MULTITARGETED CHEMICAL PROBES AND CANCER THERAPEUTICS.
JRNL REF MOL. CANCER THER. V. 16 1054 2017
JRNL REFN ESSN 1538-8514
JRNL PMID 28336808
JRNL DOI 10.1158/1535-7163.MCT-16-0568-T
REMARK 2
REMARK 2 RESOLUTION. 1.76 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
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) : 1.76
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.61
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 13221
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.156
REMARK 3 FREE R VALUE : 0.204
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010
REMARK 3 FREE R VALUE TEST SET COUNT : 662
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 31.6149 - 3.0088 1.00 2639 139 0.1564 0.1708
REMARK 3 2 3.0088 - 2.3885 1.00 2525 133 0.1631 0.2231
REMARK 3 3 2.3885 - 2.0866 1.00 2476 131 0.1422 0.2090
REMARK 3 4 2.0866 - 1.8959 1.00 2459 129 0.1486 0.2474
REMARK 3 5 1.8959 - 1.7600 1.00 2460 130 0.1548 0.2500
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) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 19.02
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.53
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 : 0.010 1137
REMARK 3 ANGLE : 1.331 1547
REMARK 3 CHIRALITY : 0.047 158
REMARK 3 PLANARITY : 0.006 196
REMARK 3 DIHEDRAL : 22.642 446
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 5F5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-15.
REMARK 100 THE DEPOSITION ID IS D_1000216079.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-AUG-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-BM
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00
REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE-CRYSTAL
REMARK 200 SI(220)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13222
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760
REMARK 200 RESOLUTION RANGE LOW (A) : 31.615
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 7.100
REMARK 200 R MERGE (I) : 0.04100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.2600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.34800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.670
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 4O78
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.69
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5 MG/ML BRD4, 5MM HEPES PH 7.5,
REMARK 280 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM,
REMARK 280 SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM MA2-014, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 17.30000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.86500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.68500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.86500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.30000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.68500
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 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 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 349 O HOH A 350 2.16
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 HZ3 LYS A 76 HE3 LYS A 155 4477 0.65
REMARK 500 HZ1 LYS A 76 HG3 LYS A 155 4477 1.01
REMARK 500 HZ2 LYS A 76 HG3 LYS A 155 4477 1.16
REMARK 500 NZ LYS A 76 HG3 LYS A 155 4477 1.32
REMARK 500 HZ3 LYS A 76 CE LYS A 155 4477 1.36
REMARK 500 NZ LYS A 76 HE3 LYS A 155 4477 1.51
REMARK 500 HZ2 LYS A 76 CG LYS A 155 4477 1.56
REMARK 500 NZ LYS A 76 CG LYS A 155 4477 1.95
REMARK 500 NZ LYS A 76 CE LYS A 155 4477 2.07
REMARK 500 NZ LYS A 76 CD LYS A 155 4477 2.17
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 5VY 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5F60 RELATED DB: PDB
REMARK 900 RELATED ID: 5F61 RELATED DB: PDB
REMARK 900 RELATED ID: 5F62 RELATED DB: PDB
REMARK 900 RELATED ID: 5F63 RELATED DB: PDB
DBREF 5F5Z A 44 168 UNP O60885 BRD4_HUMAN 44 168
SEQADV 5F5Z SER A 42 UNP O60885 EXPRESSION TAG
SEQADV 5F5Z MET A 43 UNP O60885 EXPRESSION TAG
SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN
SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU
SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA
SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN
SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP
SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR
SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET
SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP
SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU
SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU
HET 5VY A 201 71
HET EDO A 202 10
HET EDO A 203 10
HETNAM 5VY 2-METHYL-~{N}-[3-[[5-METHYL-2-[[4-(4-METHYLPIPERAZIN-1-
HETNAM 2 5VY YL)PHENYL]AMINO]PYRIMIDIN-4-YL]AMINO]PHENYL]PROPANE-2-
HETNAM 3 5VY SULFONAMIDE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 5VY C26 H35 N7 O2 S
FORMUL 3 EDO 2(C2 H6 O2)
FORMUL 5 HOH *80(H2 O)
HELIX 1 AA1 THR A 60 VAL A 69 1 10
HELIX 2 AA2 VAL A 69 HIS A 77 1 9
HELIX 3 AA3 ALA A 80 GLN A 84 5 5
HELIX 4 AA4 ASP A 96 ILE A 101 1 6
HELIX 5 AA5 ASP A 106 ASN A 116 1 11
HELIX 6 AA6 ASN A 121 ASN A 140 1 20
HELIX 7 AA7 ASP A 144 ASN A 162 1 19
SITE 1 AC1 10 TRP A 81 PRO A 82 PHE A 83 PRO A 86
SITE 2 AC1 10 VAL A 87 ASP A 88 LYS A 91 LEU A 92
SITE 3 AC1 10 LEU A 94 ASN A 140
SITE 1 AC2 4 ILE A 100 LYS A 102 THR A 103 ASN A 135
SITE 1 AC3 4 ASP A 145 ILE A 146 HOH A 328 HOH A 332
CRYST1 34.600 47.370 77.730 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 0.028902 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021110 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012865 0.00000
(ATOM LINES ARE NOT SHOWN.)
END