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- PDB-2ouo: Crystal Structure of the Bromo domain 2 in human Bromodomain Cont... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ouo | ||||||
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Title | Crystal Structure of the Bromo domain 2 in human Bromodomain Containing Protein 4 (BRD4) | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | SIGNALING PROTEIN / BRD4 / bromodomain containing protein 4 / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Filippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. ...Filippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Histone recognition and large-scale structural analysis of the human bromodomain family. Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / 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 | ![]() | 41.6 KB | Display | ![]() |
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PDB format | ![]() | 27.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.9 KB | Display | ![]() |
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Full document | ![]() | 410.4 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbC ![]() 2oo1C ![]() 2ossC ![]() 2rfjC ![]() 3d7cC ![]() 3daiC ![]() 3dwyC ![]() 3gg3C ![]() 3hmeC ![]() 3hmfC ![]() 3hmhC ![]() 3i3jC ![]() 3iu5C ![]() 3iu6C ![]() 3lxjC ![]() 3mb3C ![]() 3mb4C ![]() 3mqmC ![]() 3nxbC ![]() 3p1cC ![]() 3p1dC ![]() 3q2eC ![]() 3rcwC ![]() 3tlpC ![]() 3uv2C ![]() 3uv4C ![]() 3uv5C ![]() 3uvdC ![]() 3uvwC ![]() 3uvxC ![]() 3uvyC ![]() 3uw9C ![]() 1x0jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15060.332 Da / Num. of mol.: 1 / Fragment: Bromo domain 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M MIB, 30% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 8, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.7 % / Av σ(I) over netI: 11.4 / Number: 44952 / Rmerge(I) obs: 0.065 / Χ2: 1.03 / D res high: 1.89 Å / D res low: 50 Å / Num. obs: 12030 / % possible obs: 99.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.74→73.72 Å / Num. all: 15125 / Num. obs: 15125 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Χ2: 1.031 / Net I/σ(I): 11.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.74→1.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.618 / Num. unique all: 1156 / Χ2: 0.941 / % possible all: 98.6 |
-Phasing
Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1X0J Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.961 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.303 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.96 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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