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Yorodumi- PDB-5hem: Crystal structure of the N-terminus D161Y bromodomain mutant of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hem | ||||||
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Title | Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2 | ||||||
Components | Bromodomain-containing protein 2BRD2 | ||||||
Keywords | TRANSCRIPTION / Transcription regulation / post translational modifications recognition | ||||||
Function / homology | Function and homology information positive regulation of T-helper 17 cell lineage commitment / chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...positive regulation of T-helper 17 cell lineage commitment / chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Tallant, C. / Lori, C. / Pasquo, A. / Chiaraluce, R. / Consalvi, V. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2 Authors: Tallant, C. / Lori, C. / Pasquo, A. / Chiaraluce, R. / Consalvi, V. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hem.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hem.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/5hem ftp://data.pdbj.org/pub/pdb/validation_reports/he/5hem | HTTPS FTP |
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-Related structure data
Related structure data | 4alhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14964.523 Da / Num. of mol.: 2 / Mutation: D161Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.29 % / Description: Rod |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15% PEG3350, 0.1M bis-tris propane pH 6.6, 10% ethylene glycol, 0.15M sodium acetate PH range: 6.6-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→29.67 Å / Num. all: 33564 / Num. obs: 33564 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.108 / Rsym value: 0.05 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.1 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ALH Resolution: 1.65→29.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.2 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / 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: 16.245 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→29.67 Å
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Refine LS restraints |
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