HEADER TRANSCRIPTION 28-JUL-14 4QZS
TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN 3-FLUORO TYROSINE-
TITLE 2 LABELED BRD4 IN COMPLEX WITH JQ1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: BROMO 1 DOMAIN 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: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DL39(DE3)-PRARE;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4
KEYWDS CAP, MCAP, PROTEIN BINDING-INHIBITOR COMPLEX, MITOTIC CHROMOSOME
KEYWDS 2 ASSOCIATED PROTEIN, CELL CYCLE, INHIBITOR, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR S.W.EMBER,E.SCHONBRUNN
REVDAT 3 20-SEP-23 4QZS 1 REMARK SEQADV LINK
REVDAT 2 21-JAN-15 4QZS 1 JRNL
REVDAT 1 29-OCT-14 4QZS 0
JRNL AUTH N.K.MISHRA,A.K.URICK,S.W.EMBER,E.SCHONBRUNN,W.C.POMERANTZ
JRNL TITL FLUORINATED AROMATIC AMINO ACIDS ARE SENSITIVE (19)F NMR
JRNL TITL 2 PROBES FOR BROMODOMAIN-LIGAND INTERACTIONS.
JRNL REF ACS CHEM.BIOL. V. 9 2755 2014
JRNL REFN ISSN 1554-8929
JRNL PMID 25290579
JRNL DOI 10.1021/CB5007344
REMARK 2
REMARK 2 RESOLUTION. 1.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496)
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) : 1.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.65
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6
REMARK 3 NUMBER OF REFLECTIONS : 22235
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.140
REMARK 3 FREE R VALUE : 0.185
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1112
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 19.6510 - 2.8964 0.88 2629 139 0.1494 0.1922
REMARK 3 2 2.8964 - 2.3001 0.92 2630 138 0.1505 0.2057
REMARK 3 3 2.3001 - 2.0097 0.94 2638 139 0.1252 0.1567
REMARK 3 4 2.0097 - 1.8261 0.95 2679 141 0.1225 0.1736
REMARK 3 5 1.8261 - 1.6953 0.96 2672 141 0.1236 0.1686
REMARK 3 6 1.6953 - 1.5954 0.97 2680 140 0.1235 0.1662
REMARK 3 7 1.5954 - 1.5155 0.96 2681 142 0.1378 0.2111
REMARK 3 8 1.5155 - 1.4500 0.91 2514 132 0.1565 0.2345
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.350
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 : 0.009 1219
REMARK 3 ANGLE : 1.458 1681
REMARK 3 CHIRALITY : 0.072 168
REMARK 3 PLANARITY : 0.006 213
REMARK 3 DIHEDRAL : 15.267 447
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 4QZS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-14.
REMARK 100 THE DEPOSITION ID IS D_1000086719.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-FEB-14
REMARK 200 TEMPERATURE (KELVIN) : 93
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-ID
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 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22274
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5
REMARK 200 DATA REDUNDANCY : 5.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.07600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47
REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.33000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
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: 2OSS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.26
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13
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 HEPES PH7.5, 0.1M AMMONIUM
REMARK 280 ACETATE 12.5% PEG 3,350, 10% DMSO, 1 MM JQ1, VAPOR DIFFUSION,
REMARK 280 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 18.38350
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.29850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.44900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.29850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.38350
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.44900
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 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 HZ1 LYS A 141 O HOH A 348 1.56
REMARK 500 O HOH A 460 O HOH A 461 2.05
REMARK 500 O HOH A 413 O HOH A 446 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASN A 52 102.84 -176.19
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 JQ1 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 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 204
DBREF 4QZS A 44 168 UNP O60885 BRD4_HUMAN 44 168
SEQADV 4QZS SER A 42 UNP O60885 EXPRESSION TAG
SEQADV 4QZS 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 YOF 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 YOF YOF LYS ILE ILE LYS THR PRO MET ASP
SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN YOF YOF
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 YOF ILE YOF 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
MODRES 4QZS YOF A 65 TYR 3-FLUOROTYROSINE
MODRES 4QZS YOF A 97 TYR 3-FLUOROTYROSINE
MODRES 4QZS YOF A 98 TYR 3-FLUOROTYROSINE
MODRES 4QZS YOF A 118 TYR 3-FLUOROTYROSINE
MODRES 4QZS YOF A 119 TYR 3-FLUOROTYROSINE
MODRES 4QZS YOF A 137 TYR 3-FLUOROTYROSINE
MODRES 4QZS YOF A 139 TYR 3-FLUOROTYROSINE
HET YOF A 65 13
HET YOF A 97 23
HET YOF A 98 23
HET YOF A 118 13
HET YOF A 119 23
HET YOF A 137 23
HET YOF A 139 13
HET JQ1 A 201 31
HET EDO A 202 10
HET EDO A 203 10
HET CL A 204 1
HETNAM YOF 3-FLUOROTYROSINE
HETNAM JQ1 (6S)-6-(2-TERT-BUTOXY-2-OXOETHYL)-4-(4-CHLOROPHENYL)-2,
HETNAM 2 JQ1 3,9-TRIMETHYL-6,7-DIHYDROTHIENO[3,2-F][1,2,
HETNAM 3 JQ1 4]TRIAZOLO[4,3-A][1,4]DIAZEPIN-10-IUM
HETNAM EDO 1,2-ETHANEDIOL
HETNAM CL CHLORIDE ION
HETSYN EDO ETHYLENE GLYCOL
FORMUL 1 YOF 7(C9 H10 F N O3)
FORMUL 2 JQ1 C23 H26 CL N4 O2 S 1+
FORMUL 3 EDO 2(C2 H6 O2)
FORMUL 5 CL CL 1-
FORMUL 6 HOH *172(H2 O)
HELIX 1 1 THR A 60 VAL A 69 1 10
HELIX 2 2 VAL A 69 HIS A 77 1 9
HELIX 3 3 ALA A 80 GLN A 84 5 5
HELIX 4 4 ASP A 96 ILE A 101 1 6
HELIX 5 5 ASP A 106 ASN A 116 1 11
HELIX 6 6 ASN A 121 ASN A 140 1 20
HELIX 7 7 ASP A 144 ASN A 162 1 19
LINK C GLN A 64 N YOF A 65 1555 1555 1.33
LINK C YOF A 65 N LEU A 66 1555 1555 1.33
LINK C ASP A 96 N YOF A 97 1555 1555 1.33
LINK C YOF A 97 N YOF A 98 1555 1555 1.33
LINK C YOF A 98 N LYS A 99 1555 1555 1.34
LINK C ASN A 117 N YOF A 118 1555 1555 1.33
LINK C YOF A 118 N YOF A 119 1555 1555 1.33
LINK C YOF A 119 N TRP A 120 1555 1555 1.34
LINK C CYS A 136 N YOF A 137 1555 1555 1.32
LINK C YOF A 137 N ILE A 138 1555 1555 1.34
LINK C ILE A 138 N YOF A 139 1555 1555 1.33
LINK C YOF A 139 N ASN A 140 1555 1555 1.33
SITE 1 AC1 11 PRO A 53 TRP A 81 PRO A 82 YOF A 97
SITE 2 AC1 11 LYS A 99 YOF A 139 ASN A 140 ILE A 146
SITE 3 AC1 11 MET A 149 HOH A 301 HOH A 340
SITE 1 AC2 5 ILE A 100 ILE A 101 LYS A 102 THR A 103
SITE 2 AC2 5 ASN A 135
SITE 1 AC3 2 YOF A 65 HOH A 396
SITE 1 AC4 5 SER A 51 ASN A 52 LYS A 57 ASP A 145
SITE 2 AC4 5 HOH A 400
CRYST1 36.767 44.898 78.597 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 0.027198 0.000000 0.000000 0.00000
SCALE2 0.000000 0.022273 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012723 0.00000
(ATOM LINES ARE NOT SHOWN.)
END