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- PDB-6y7h: Structure of the BRD9 bromodomain and compound 11 -

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Basic information

Entry
Database: PDB / ID: 6y7h
TitleStructure of the BRD9 bromodomain and compound 11
ComponentsBromodomain-containing protein 9
KeywordsSTRUCTURAL GENOMICS / BRD9 / Bromodomain-containing protein 9 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
1-(8-phenylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDiaz-Saez, L. / Krojer, T. / Picaud, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative
CitationJournal: To Be Published
Title: Structure of the BRD9 bromodomain
Authors: Diaz-Saez, L. / Krojer, T. / Picaud, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M.
History
DepositionMar 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7848
Polymers28,0632
Non-polymers7216
Water3,549197
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5166
Polymers14,0311
Non-polymers4855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2682
Polymers14,0311
Non-polymers2361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.610, 38.310, 60.940
Angle α, β, γ (deg.)90.000, 107.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 14031.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R2 / References: UniProt: Q9H8M2
#2: Chemical ChemComp-OFK / 1-(8-phenylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone


Mass: 236.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M ammonium sulfate, 30% pentaerythritol ethoxylate 15/4, 0.1M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.8→58.26 Å / Num. obs: 24177 / % possible obs: 99.4 % / Redundancy: 3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.057 / Rrim(I) all: 0.102 / Net I/σ(I): 7.2 / Num. measured all: 72790 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.842.80.449408914420.4050.3170.5522.299.2
9-58.263.20.0357022220.9980.0220.04121.399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å58.26 Å
Translation2.5 Å58.26 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQ1

5mq1


Resolution: 1.8→58.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.879 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1139 4.7 %RANDOM
Rwork0.1837 ---
obs0.1858 23026 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.86 Å2 / Biso mean: 28.807 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å2-0.32 Å2
2---0.18 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 1.8→58.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 52 197 2079
Biso mean--40.11 35.15 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191999
X-RAY DIFFRACTIONr_bond_other_d0.0020.021999
X-RAY DIFFRACTIONr_angle_refined_deg1.882.0012692
X-RAY DIFFRACTIONr_angle_other_deg1.0713.0034606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0625236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4542380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70815383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5391511
X-RAY DIFFRACTIONr_chiral_restr0.110.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 83 -
Rwork0.326 1702 -
all-1785 -
obs--99.22 %

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