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- PDB-2oo1: Crystal structure of the Bromo domain 2 of human Bromodomain cont... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oo1 | ||||||
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Title | Crystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (BRD3) | ||||||
![]() | Bromodomain-containing protein 3 | ||||||
![]() | SIGNALING PROTEIN / BRD3 / bromodomain containing protein 3 / ORFX / RING3 like gene / RING3L / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Filippakopoulos, P. / Bullock, A. / Papagrigoriou, E. / Keates, T. / Cooper, C. / Smee, C. / Ugochukwu, E. / Debreczeni, J. / von Delft, F. / Arrowsmith, C. ...Filippakopoulos, P. / Bullock, A. / Papagrigoriou, E. / Keates, T. / Cooper, C. / Smee, C. / Ugochukwu, E. / Debreczeni, J. / von Delft, F. / Arrowsmith, C. / 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 | ![]() | 115.5 KB | Display | ![]() |
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PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 741.7 KB | Display | ![]() |
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Full document | ![]() | 745.1 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbC ![]() 2ossC ![]() 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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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
#1: Protein | Mass: 13307.399 Da / Num. of mol.: 4 / Fragment: Bromo 2 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-7PE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, 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: Nov 26, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 4.9 % / Av σ(I) over netI: 6.6 / Number: 335488 / Rmerge(I) obs: 0.094 / Χ2: 1.06 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 69114 / % possible obs: 99.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.7→50 Å / Num. all: 69322 / Num. obs: 69114 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Χ2: 1.061 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.1 % / Num. unique all: 6853 / Χ2: 0.929 / % 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: 1.7→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.943 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The molecule 7PE should be a polyethylene glycol 3350. Only the fragment has been built due to electron density that was incomplete for full assignment.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.332 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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