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- PDB-6bqa: BRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-d... -

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Basic information

Entry
Database: PDB / ID: 6bqa
TitleBRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide
ComponentsBromodomain-containing protein 9
KeywordsGENE REGULATION / BRD9 / Bromodomain
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-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-67C / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.031 Å
AuthorsMurray, J.M. / Tang, Y.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2019
Title: Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.
Authors: Nittinger, E. / Gibbons, P. / Eigenbrot, C. / Davies, D.R. / Maurer, B. / Yu, C.L. / Kiefer, J.R. / Kuglstatter, A. / Murray, J. / Ortwine, D.F. / Tang, Y. / Tsui, V.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1922
Polymers11,8571
Non-polymers3351
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.785, 34.114, 39.867
Angle α, β, γ (deg.)70.250, 74.140, 74.560
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11856.921 Da / Num. of mol.: 1 / Fragment: BRD9 bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-67C / 3-[6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl]-N,N-dimethylbenzamide


Mass: 335.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5, 20% PEG 2000 monomethylether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.031→50 Å / Num. obs: 51882 / % possible obs: 90.76 % / Redundancy: 3.1 % / Net I/σ(I): 12
Reflection shellResolution: 1.0311→1.04 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
PHASERphasing
PHENIXdev_2747refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5I40

5i40


Resolution: 1.031→12.819 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 16.69
RfactorNum. reflection% reflection
Rfree0.1712 2597 5.01 %
Rwork0.1621 --
obs0.1626 51882 90.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.99 Å2 / Biso mean: 15.298 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 1.031→12.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 46 227 1103
Biso mean--13.05 21.31 -
Num. residues----102
Refinement TLS params.Method: refined / Origin x: -52.772 Å / Origin y: -36.347 Å / Origin z: -3.963 Å
111213212223313233
T0.0943 Å20.0006 Å2-0.0023 Å2-0.088 Å20.0047 Å2--0.0847 Å2
L0.8361 °2-0.0007 °2-0.072 °2-0.5036 °20.0023 °2--0.2722 °2
S0.0292 Å °-0.0203 Å °-0.0084 Å °-0.0169 Å °-0.0177 Å °0.0155 Å °0.0167 Å °-0.0227 Å °0.0001 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 22:123 )

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