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Yorodumi- PDB-3hme: Crystal structure of human bromodomain containing 9 isoform 1 (BRD9) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hme | ||||||
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Title | Crystal structure of human bromodomain containing 9 isoform 1 (BRD9) | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | SIGNALING PROTEIN / BRD9 / bromodomain containing 9 isoform 1 / LAVS3040 / PRO9856 / Rhabdomyosarcoma antigen MU-RMS-40.8 / Sarcoma antigen NY-SAR-29 / Bromodomain / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å | ||||||
Authors | Filippakopoulos, P. / Eswaran, J. / Keates, T. / Picaud, S. / Roos, A. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. ...Filippakopoulos, P. / Eswaran, J. / Keates, T. / Picaud, S. / Roos, A. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: Histone recognition and large-scale structural analysis of the human bromodomain family. Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hme.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hme.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/3hme ftp://data.pdbj.org/pub/pdb/validation_reports/hm/3hme | HTTPS FTP |
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-Related structure data
Related structure data | 2nxbSC 2oo1SC 2ossSC 2ouoSC 2rfjSC 3d7cSC 3daiSC 3dwySC 3gg3C 3hmfC 3hmhC 3i3jC 3iu5C 3iu6C 3lxjC 3mb3C 3mb4C 3mqmC 3nxbC 3p1cC 3p1dC 3q2eC 3rcwC 3tlpC 3uv2C 3uv4C 3uv5C 3uvdC 3uvwC 3uvxC 3uvyC 3uw9C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: Bromodomain, 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) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9H8M2 #2: 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: 2.34 Å3/Da / Density % sol: 47.5 % / Mosaicity: 0.63 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25.5% PEG 3350, 0.17M (NH4)2SO4, 15% glyc, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→35.62 Å / Num. all: 13809 / Num. obs: 13436 / % possible obs: 97.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.23→2.35 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1608 / Rsym value: 0.598 / % possible all: 81.8 |
-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR | Rfactor: 46.59 / Model details: Phaser MODE: MR_AUTO
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 14108 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY Resolution: 2.23→35.62 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.205 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.835 / SU B: 14.676 / SU ML: 0.165 / SU R Cruickshank DPI: 0.306 / SU Rfree: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.75 Å2 / Biso mean: 15.001 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.23→35.62 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.23→2.288 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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