+Open data
-Basic information
Entry | Database: PDB / ID: 6y7i | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the BRD9 bromodomain and compound 2 | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | STRUCTURAL GENOMICS / BRD9 / Bromodomain-containing protein 9 / Structural Genomics Consortium / SGC | ||||||
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: 1.6 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. / Structural Genomics Consortium (SGC) | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of the BRD9 bromodomain and compound 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6y7i.cif.gz | 71 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6y7i.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 6y7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y7i_validation.pdf.gz | 1022.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6y7i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6y7i_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6y7i_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/6y7i ftp://data.pdbj.org/pub/pdb/validation_reports/y7/6y7i | HTTPS FTP |
-Related structure data
Related structure data | 6y7lC 5mq1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 14031.487 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
---|---|
Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6.5 Details: 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.02M sodium/potassium phosphate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.6→58.14 Å / Num. obs: 33726 / % possible obs: 98.8 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.036 / Rrim(I) all: 0.064 / Net I/σ(I): 8.5 / Num. measured all: 96900 / Scaling rejects: 3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MQ1 Resolution: 1.6→58.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.31 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.12 Å2 / Biso mean: 24.773 Å2 / Biso min: 11.19 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→58.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 7200 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|