+Open data
-Basic information
Entry | Database: PDB / ID: 5o3e | ||||||||||||
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Title | Human Brd2(BD2) mutant in complex with Me-Am1 | ||||||||||||
Components | Bromodomain-containing protein 2 | ||||||||||||
Keywords | TRANSCRIPTION / The Bromodomain and Extra-Terminal Domain (BET) Family Chromatin binding protein | ||||||||||||
Function / homology | Function and homology information acetylation-dependent protein binding / chromatin looping / positive regulation of T-helper 17 cell lineage commitment / RUNX3 regulates p14-ARF / protein localization to chromatin / lysine-acetylated histone binding / neural tube closure / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / positive regulation of T-helper 17 cell lineage commitment / RUNX3 regulates p14-ARF / protein localization to chromatin / lysine-acetylated histone binding / neural tube closure / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Chan, K.-H. / Runcie, A.C. / Ciulli, A. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Chem Sci / Year: 2018 Title: Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition. Authors: Runcie, A.C. / Zengerle, M. / Chan, K.H. / Testa, A. / van Beurden, L. / Baud, M.G.J. / Epemolu, O. / Ellis, L.C.J. / Read, K.D. / Coulthard, V. / Brien, A. / Ciulli, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o3e.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o3e.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o3e ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o3e | HTTPS FTP |
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-Related structure data
Related structure data | 5o38C 5o39C 5o3aC 5o3bC 5o3cC 5o3dC 5o3fC 5o3gC 5o3hC 5o3iC 4qeuS 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: 13361.383 Da / Num. of mol.: 1 / Fragment: UNP residues 344-455 / Mutation: L383V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P25440 |
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#2: Chemical | ChemComp-9HW / ( |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-DQW / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris pH 7.75 55% Pentaerythritol propoxylate (5/4 PO/OH) 0.2M Imidazole pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→35.98 Å / Num. obs: 24337 / % possible obs: 99.77 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1005 / Net I/σ(I): 15.07 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.2228 / Num. unique obs: 2352 / CC1/2: 0.955 / % possible all: 97.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QEU Resolution: 1.4→35.975 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→35.975 Å
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Refine LS restraints |
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LS refinement shell |
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