+Open data
-Basic information
Entry | Database: PDB / ID: 6y7k | ||||||
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Title | Structure of the BRD9 bromodomain and compound 27 | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | STRUCTURAL GENOMICS / BRD9 / Bromodomain-containing protein 9 | ||||||
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 / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Diaz-Saez, L. / Krojer, T. / Picaud, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y7k.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y7k.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 6y7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y7k_validation.pdf.gz | 774.6 KB | Display | wwPDB validaton report |
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Full document | 6y7k_full_validation.pdf.gz | 778.2 KB | Display | |
Data in XML | 6y7k_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 6y7k_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/6y7k ftp://data.pdbj.org/pub/pdb/validation_reports/y7/6y7k | HTTPS FTP |
-Related structure data
Related structure data | 6y7hC 6y7jC 5mq1S 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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-Components
#1: Protein | Mass: 14031.487 Da / Num. of mol.: 1 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 | ||||||
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#2: Chemical | ChemComp-OEZ / ~{ | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350,10% ethylene glycol, 0.1M bis-tris-propane pH 7.5, 0.2M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→53.14 Å / Num. obs: 39068 / % possible obs: 94.7 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.025 / Rrim(I) all: 0.046 / Net I/σ(I): 17.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MQ1 Resolution: 1.2→53.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.889 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.037 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.54 Å2 / Biso mean: 14.802 Å2 / Biso min: 5.29 Å2
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Refinement step | Cycle: final / Resolution: 1.2→53.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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