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Yorodumi- PDB-2oo1: Crystal structure of the Bromo domain 2 of human Bromodomain cont... -
+Open data
-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) | ||||||
Components | Bromodomain-containing protein 3 | ||||||
Keywords | SIGNALING PROTEIN / BRD3 / bromodomain containing protein 3 / ORFX / RING3 like gene / RING3L / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oo1.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oo1.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/2oo1 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/2oo1 | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3 / References: UniProt: Q15059 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-7PE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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