+Open data
-Basic information
Entry | Database: PDB / ID: 5o38 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human Brd2(BD2) mutant in free form | ||||||||||||
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 / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / 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: 1.2 Å | ||||||||||||
Authors | Chan, K.-H. / Runcie, A.C. / Ciulli, A. | ||||||||||||
Funding support | United Kingdom, 3items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5o38.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5o38.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o38 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o38 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5o39C 5o3aC 5o3bC 5o3cC 5o3dC 5o3eC 5o3fC 5o3gC 5o3hC 5o3iC 4qeuS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13361.383 Da / Num. of mol.: 1 / Mutation: L383V 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 BL21 (bacteria) / References: UniProt: P25440 |
---|---|
#2: Chemical | ChemComp-9JB / |
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris pH8.0 50% Pentaerythritol propoxylate (5/4 PO/OH) 0.2M Imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.5 Å / Num. obs: 37657 / % possible obs: 98.26 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02237 / Net I/σ(I): 15.57 |
Reflection shell | Resolution: 1.2→1.243 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.08386 / Mean I/σ(I) obs: 6.62 / Num. unique obs: 3520 / CC1/2: 0.974 / % possible all: 93.37 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QEU Resolution: 1.2→19.499 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.14 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→19.499 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|