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- PDB-5n2l: Crystal structure of the second bromodomain of human BRD2 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n2l | ||||||
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Title | Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue | ||||||
![]() | Bromodomain-containing protein 2 | ||||||
![]() | TRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() 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 phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. ...Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. / Picaud, S. / Fedorov, O. / Krojer, T. / Chen, T. / Lee, R.E. / Guy, R.K. / Shelat, A.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue Authors: Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. / Picaud, S. / Fedorov, O. / Krojer, T. / Chen, ...Authors: Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. / Picaud, S. / Fedorov, O. / Krojer, T. / Chen, T. / Lee, R.E. / Guy, R.K. / Shelat, A.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.1 KB | Display | ![]() |
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PDB format | ![]() | 159.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dvvS S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13375.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-8J2 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG3350, 0.2 M ammonium sulfate, 0.1 M Bis-tris pH 5.5 PH range: 5.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→28.95 Å / Num. obs: 41476 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.519 Å2 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.131 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.89→1.94 Å / Redundancy: 6 % / Rmerge(I) obs: 1.914 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2554 / Rpim(I) all: 1.286 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DVV Resolution: 1.89→28.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.978 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.587 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→28.95 Å
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Refine LS restraints |
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