[English] 日本語
Yorodumi- PDB-5ign: Crystal structure of human BRD9 bromodomain in complex with LP99 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ign | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | TRANSCRIPTION / lysine-acetylated histone binding / chromatin regulator / Structural Genomics / 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 / regulation of transcription by RNA polymerase II / chromatin ...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 / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tallant, C. / Clark, P.G.K. / Vieira, L.C.C. / Newman, J.A. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. ...Tallant, C. / Clark, P.G.K. / Vieira, L.C.C. / Newman, J.A. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of BRD9 bromodomain in complex with LP99 chemical probe Authors: Tallant, C. / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ign.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ign.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ign.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ign_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ign_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5ign_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5ign_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/5ign ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5ign | HTTPS FTP |
-Related structure data
Related structure data | 3hmeS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: UNP residues 14-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.55 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M sodium nitrate, 0.1 M bis tris propane pH 8.5, 20% PEG 3350, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28.93 Å / Num. obs: 27716 / % possible obs: 99.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 6.873 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.045 / Net I/av σ(I): 15.5 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 3.2 / % possible all: 97.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HME Resolution: 1.7→28.93 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.715 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.157 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→28.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|