HEADER GENE REGULATION 27-NOV-17 6BQA
TITLE BRD9 BROMODOMAIN IN COMPLEX WITH 3-(6-(BUT-3-EN-1-YL)-7-OXO-6,7-
TITLE 2 DIHYDRO-1H-PYRROLO[2,3-C]PYRIDIN-4-YL)-N,N-DIMETHYLBENZAMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 9;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: BRD9 BROMODOMAIN;
COMPND 5 SYNONYM: RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8;
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: BRD9, UNQ3040/PRO9856;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS BRD9, BROMODOMAIN, GENE REGULATION
EXPDTA X-RAY DIFFRACTION
AUTHOR J.M.MURRAY,Y.TANG
REVDAT 4 04-OCT-23 6BQA 1 JRNL
REVDAT 3 27-MAR-19 6BQA 1 JRNL
REVDAT 2 27-FEB-19 6BQA 1 JRNL
REVDAT 1 14-NOV-18 6BQA 0
JRNL AUTH E.NITTINGER,P.GIBBONS,C.EIGENBROT,D.R.DAVIES,B.MAURER,
JRNL AUTH 2 C.L.YU,J.R.KIEFER,A.KUGLSTATTER,J.MURRAY,D.F.ORTWINE,Y.TANG,
JRNL AUTH 3 V.TSUI
JRNL TITL WATER MOLECULES IN PROTEIN-LIGAND INTERFACES. EVALUATION OF
JRNL TITL 2 SOFTWARE TOOLS AND SAR COMPARISON.
JRNL REF J. COMPUT. AIDED MOL. DES. V. 33 307 2019
JRNL REFN ESSN 1573-4951
JRNL PMID 30756207
JRNL DOI 10.1007/S10822-019-00187-Y
REMARK 2
REMARK 2 RESOLUTION. 1.03 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX DEV_2747
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) : 1.03
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.82
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8
REMARK 3 NUMBER OF REFLECTIONS : 51882
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.163
REMARK 3 R VALUE (WORKING SET) : 0.162
REMARK 3 FREE R VALUE : 0.171
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010
REMARK 3 FREE R VALUE TEST SET COUNT : 2597
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
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) : 0.090
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.690
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.30
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ( CHAIN A AND RESID 22:123 )
REMARK 3 ORIGIN FOR THE GROUP (A): -52.772 -36.347 -3.963
REMARK 3 T TENSOR
REMARK 3 T11: 0.0943 T22: 0.0880
REMARK 3 T33: 0.0847 T12: 0.0006
REMARK 3 T13: -0.0023 T23: 0.0047
REMARK 3 L TENSOR
REMARK 3 L11: 0.8361 L22: 0.5036
REMARK 3 L33: 0.2722 L12: -0.0007
REMARK 3 L13: -0.0720 L23: 0.0023
REMARK 3 S TENSOR
REMARK 3 S11: 0.0292 S12: -0.0203 S13: -0.0084
REMARK 3 S21: -0.0169 S22: -0.0177 S23: 0.0155
REMARK 3 S31: 0.0167 S32: -0.0227 S33: 0.0001
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 6BQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-17.
REMARK 100 THE DEPOSITION ID IS D_1000231272.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-MAR-15
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 : 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) : 0.9793
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51882
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.031
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8
REMARK 200 DATA REDUNDANCY : 3.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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
REMARK 200 STARTING MODEL: PDBID 5I40
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, PH 6.5, 20% PEG 2000
REMARK 280 MONOMETHYLETHER, VAPOR DIFFUSION, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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 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 A 525 DISTANCE = 5.81 ANGSTROMS
REMARK 525 HOH A 526 DISTANCE = 6.21 ANGSTROMS
REMARK 525 HOH A 527 DISTANCE = 6.65 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 67C A 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6BQD RELATED DB: PDB
DBREF 6BQA A 22 123 UNP Q9H8M2 BRD9_HUMAN 138 239
SEQRES 1 A 102 SER THR PRO ILE GLN GLN LEU LEU GLU HIS PHE LEU ARG
SEQRES 2 A 102 GLN LEU GLN ARG LYS ASP PRO HIS GLY PHE PHE ALA PHE
SEQRES 3 A 102 PRO VAL THR ASP ALA ILE ALA PRO GLY TYR SER MET ILE
SEQRES 4 A 102 ILE LYS HIS PRO MET ASP PHE GLY THR MET LYS ASP LYS
SEQRES 5 A 102 ILE VAL ALA ASN GLU TYR LYS SER VAL THR GLU PHE LYS
SEQRES 6 A 102 ALA ASP PHE LYS LEU MET CYS ASP ASN ALA MET THR TYR
SEQRES 7 A 102 ASN ARG PRO ASP THR VAL TYR TYR LYS LEU ALA LYS LYS
SEQRES 8 A 102 ILE LEU HIS ALA GLY PHE LYS MET MET SER LYS
HET 67C A 201 46
HETNAM 67C 3-[6-(BUT-3-EN-1-YL)-7-OXO-6,7-DIHYDRO-1H-PYRROLO[2,3-
HETNAM 2 67C C]PYRIDIN-4-YL]-N,N-DIMETHYLBENZAMIDE
FORMUL 2 67C C20 H21 N3 O2
FORMUL 3 HOH *227(H2 O)
HELIX 1 AA1 THR A 23 ARG A 38 1 16
HELIX 2 AA2 GLY A 56 ILE A 61 1 6
HELIX 3 AA3 ASP A 66 ALA A 76 1 11
HELIX 4 AA4 SER A 81 ASN A 100 1 20
HELIX 5 AA5 THR A 104 LYS A 123 1 20
SITE 1 AC1 9 PHE A 44 PHE A 45 VAL A 49 ILE A 53
SITE 2 AC1 9 ASN A 100 TYR A 106 LYS A 111 HOH A 305
SITE 3 AC1 9 HOH A 408
CRYST1 24.785 34.114 39.867 70.25 74.14 74.56 P 1 1
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 0.040347 -0.011147 -0.008635 0.00000
SCALE2 0.000000 0.030412 -0.009078 0.00000
SCALE3 0.000000 0.000000 0.027213 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
