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Yorodumi- PDB-6v0s: Crystal structure of the bromodomain of human BRD9 bound to TG003 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v0s | ||||||
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Title | Crystal structure of the bromodomain of human BRD9 bound to TG003 | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | GENE REGULATION / BRD9 / mSWI/SNF / BAF / non-BET / BRD / TG003 | ||||||
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: 2.4 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 | 6v0s.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v0s.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v0s_validation.pdf.gz | 364.6 KB | Display | wwPDB validaton report |
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Full document | 6v0s_full_validation.pdf.gz | 367.2 KB | Display | |
Data in XML | 6v0s_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6v0s_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/6v0s ftp://data.pdbj.org/pub/pdb/validation_reports/v0/6v0s | HTTPS FTP |
-Related structure data
Related structure data | 6ppaC 6uzfC 6v0qC 6v0uC 6v0xC 6v14C 6v16C 6v17C 6v1bC 6v1eC 6v1fC 6v1hC 6v1kC 6v1lC 6v1uC 3hmeS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 138 - 250 / Label seq-ID: 11 - 123
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-Components
#1: Protein | Mass: 14249.763 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q9H8M2 #2: Chemical | #3: 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: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 291 K / Method: evaporation Details: 0.2 M Li2SO4, 0.1 M HEPES (pH 7.5), 25% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2017 | |||||||||||||||||||||||||||
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.4→74.63 Å / Num. obs: 12097 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.011 / Rrim(I) all: 0.036 / Net I/σ(I): 37.4 / Num. measured all: 128464 / Scaling rejects: 6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.8
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HME Resolution: 2.4→37.317 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.63 Å2 / Biso mean: 79.3364 Å2 / Biso min: 44.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→37.317 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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