+Open data
-Basic information
Entry | Database: PDB / ID: 4yy4 | ||||||
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Title | Crystal structure of BRD9 Bromodomain bound to DMSO | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | PROTEIN BINDING / complex | ||||||
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: 1.47 Å | ||||||
Authors | Tang, Y. / Bellon, S. / Cochran, A.G. / Poy, F. | ||||||
Citation | Journal: Structure / Year: 2015 Title: A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Authors: Flynn, E.M. / Huang, O.W. / Poy, F. / Oppikofer, M. / Bellon, S.F. / Tang, Y. / Cochran, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yy4.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yy4.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yy4_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 4yy4_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 4yy4_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 4yy4_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/4yy4 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yy4 | HTTPS FTP |
-Related structure data
Related structure data | 4yy6C 4yydC 4yygC 4yyhC 4yyiC 4yyjC 4yykC 4yymC 4yynC 3hmeS C: citing same article (ref.) S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12444.461 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 17-123) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H8M2 |
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#2: Chemical | ChemComp-DMS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 25% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 2, 2012 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→50 Å / Num. obs: 21295 / % possible obs: 96.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Χ2: 1.04 / Net I/av σ(I): 29.094 / Net I/σ(I): 10.6 / Num. measured all: 123026 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3HME Resolution: 1.47→32.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.699 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.87 Å2 / Biso mean: 28.83 Å2 / Biso min: 15.16 Å2
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Refinement step | Cycle: final / Resolution: 1.47→32.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.471→1.509 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.4286 Å / Origin y: 12.125 Å / Origin z: 13.3628 Å
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