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- PDB-7lb4: Crystal structure of the second bromodomain (BD2) of human BRD3 b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lb4 | ||||||
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Title | Crystal structure of the second bromodomain (BD2) of human BRD3 bound to bromosporine | ||||||
![]() | Bromodomain-containing protein 3 | ||||||
![]() | GENE REGULATION/INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex | ||||||
Function / homology | ![]() lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karim, M.R. / Bikowitz, M.J. / Schonbrunn, E. | ||||||
![]() | ![]() Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 84.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 943.3 KB | Display | ![]() |
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Full document | ![]() | 946.9 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v67C ![]() 5vboC ![]() 5vbpC ![]() 5vbqC ![]() 5vbrC ![]() 7bjyC ![]() 7k6gC ![]() 7k6hC ![]() 7ko0C ![]() 7l6dC ![]() 7l72C ![]() 7l73C ![]() 7l9gC ![]() 7l9jC ![]() 7l9kC ![]() 7l9lSC ![]() 7lahC ![]() 7laiC ![]() 7lajC ![]() 7lakC ![]() 7lauC ![]() 7layC ![]() 7lazC ![]() 7lbtC ![]() 7lejC ![]() 7lekC ![]() 7lelC ![]() 7lemC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 13307.399 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 6,000, 5 % v/v (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→100 Å / Num. obs: 15413 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.048 / Rrim(I) all: 0.092 / Χ2: 1.121 / Net I/σ(I): 8.9 / Num. measured all: 56172 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7L9L Resolution: 2.004→38.135 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.73 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.41 Å2 / Biso mean: 30.5032 Å2 / Biso min: 15.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.004→38.135 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -14.669 Å / Origin y: 16.0599 Å / Origin z: -15.3597 Å
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Refinement TLS group |
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