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Yorodumi- PDB-5igm: Crystal structure of the bromodomain of human BRD9 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5igm | ||||||
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Title | Crystal structure of the bromodomain of human BRD9 in complex with bromosporine (BSP) | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | TRANSCRIPTION / chromatin remodeling / 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 / 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: 1.6 Å | ||||||
Authors | Tallant, C. / Filippakopoulos, P. / Picaud, S. / Nunez-Alonso, G. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Authors: Picaud, S. / Leonards, K. / Lambert, J.P. / Dovey, O. / Wells, C. / Fedorov, O. / Monteiro, O. / Fujisawa, T. / Wang, C.Y. / Lingard, H. / Tallant, C. / Nikbin, N. / Guetzoyan, L. / Ingham, ...Authors: Picaud, S. / Leonards, K. / Lambert, J.P. / Dovey, O. / Wells, C. / Fedorov, O. / Monteiro, O. / Fujisawa, T. / Wang, C.Y. / Lingard, H. / Tallant, C. / Nikbin, N. / Guetzoyan, L. / Ingham, R. / Ley, S.V. / Brennan, P. / Muller, S. / Samsonova, A. / Gingras, A.C. / Schwaller, J. / Vassiliou, G. / Knapp, S. / Filippakopoulos, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5igm.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5igm.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 5igm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5igm_validation.pdf.gz | 924 KB | Display | wwPDB validaton report |
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Full document | 5igm_full_validation.pdf.gz | 925.5 KB | Display | |
Data in XML | 5igm_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5igm_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/5igm ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igm | HTTPS FTP |
-Related structure data
Related structure data | 5igkC 5iglC 2grcS 2nxbS 2oo1S 2ossS 2ouoS 2rfjS 3d7cS 3daiS 3dwyS 3hmeS 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 on special symmetry positions |
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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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M bis tris pH 5.5, 0.2 M sodium chloride, 25% PEG3350 PH range: 5.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.98 Å / Num. obs: 35807 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.029 / Rsym value: 0.012 / Net I/av σ(I): 28 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HME, 2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY Resolution: 1.6→28.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.774 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.381 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→28.69 Å
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Refine LS restraints |
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