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- PDB-2oss: Crystal structure of the Bromo domain 1 in human Bromodomain Cont... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oss | ||||||
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Title | Crystal structure of the Bromo domain 1 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. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. ...Filippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Pike, A.C.W. / 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 | ![]() | 77.6 KB | Display | ![]() |
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PDB format | ![]() | 56.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.3 KB | Display | ![]() |
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Full document | ![]() | 432.7 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbC ![]() 2oo1C ![]() 2ouoC ![]() 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 S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: Bromo domain 1 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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M NaNO3, 20% PEG3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 8.1 % / Av σ(I) over netI: 14.1 / Number: 237706 / Rmerge(I) obs: 0.071 / Χ2: 1.01 / D res high: 1.35 Å / D res low: 50 Å / Num. obs: 29320 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.35→50 Å / Num. all: 29349 / Num. obs: 29320 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Χ2: 1.015 / Net I/σ(I): 14.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.177 / Num. unique all: 2874 / Χ2: 1.038 / % possible all: 100 |
-Phasing
Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1X0J Resolution: 1.35→39.19 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.361 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.052 / 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: 8.628 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→39.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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