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Yorodumi- PDB-6v1b: Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v1b | ||||||
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Title | Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | GENE REGULATION / BRD9 / mSWI/SNF / BAF / non-BET / BRD / Rhabdomyosarcoma antigen / I-BRD9 / IBRD9 | ||||||
Function / homology | Function and homology information GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Karim, M.R. / Chan, A. / Schonbrunn, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains. Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v1b.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v1b.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v1b_validation.pdf.gz | 398.4 KB | Display | wwPDB validaton report |
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Full document | 6v1b_full_validation.pdf.gz | 403.2 KB | Display | |
Data in XML | 6v1b_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 6v1b_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/6v1b ftp://data.pdbj.org/pub/pdb/validation_reports/v1/6v1b | HTTPS FTP |
-Related structure data
Related structure data | 6ppaC 6uzfSC 6v0qC 6v0sC 6v0uC 6v0xC 6v14C 6v16C 6v17C 6v1eC 6v1fC 6v1hC 6v1kC 6v1lC 6v1uC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14249.763 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: I-BRD9 / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q9H8M2 #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M KSCN, 30% w/v PEG MME 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→57.61 Å / Num. obs: 53866 / % possible obs: 97.4 % / Redundancy: 3.73 % / Biso Wilson estimate: 25.997 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 1.061 / Net I/σ(I): 12.83 / Num. measured all: 200920 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UZF Resolution: 1.35→57.61 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 198.7 Å2 / Biso mean: 34.3932 Å2 / Biso min: 12.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→57.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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