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Yorodumi- PDB-5e9v: Crystal structure of BRD9 bromodomain in complex with an indolizi... -
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-Basic information
Entry | Database: PDB / ID: 5e9v | ||||||
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Title | Crystal structure of BRD9 bromodomain in complex with an indolizine ligand | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | TRANSCRIPTION / Bromodomain / chromatin regulation | ||||||
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: 1.8 Å | ||||||
Authors | Tallant, C. / Hay, D.A. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Schofield, C.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Hay, D.A. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Schofield, C.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of BRD9 bromodomain in complex with an indolizine ligand Authors: Tallant, C. / Hay, D.A. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Schofield, C.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e9v.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e9v.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e9v_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5e9v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5e9v_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 5e9v_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/5e9v ftp://data.pdbj.org/pub/pdb/validation_reports/e9/5e9v | HTTPS FTP |
-Related structure data
Related structure data | 3hmeS 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
#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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M NaNO3, 0.1 M BTProp pH 6.5, 20% PEG 3350, 10% EtGly PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.66 Å / Num. obs: 23830 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.065 / Rsym value: 0.041 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.9 / % possible all: 96.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HME Resolution: 1.8→29.66 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.207 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 27.681 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→29.66 Å
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