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Yorodumi- PDB-3oni: Crystal Structure of the second bromodomain of human BRD2 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oni | ||||||
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Title | Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor JQ1 | ||||||
Components | Bromodomain containing 2, isoform CRA_a | ||||||
Keywords | CELL CYCLE / Structural Genomics / Structural Genomics Consortium / SGC / Bromodomain / Inhibition / Probe | ||||||
Function / homology | Function and homology information 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 serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bradner, J.E. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nature / Year: 2010 Title: Selective inhibition of BET bromodomains. Authors: Filippakopoulos, P. / Qi, J. / Picaud, S. / Shen, Y. / Smith, W.B. / Fedorov, O. / Morse, E.M. / Keates, T. / Hickman, T.T. / Felletar, I. / Philpott, M. / Munro, S. / McKeown, M.R. / Wang, ...Authors: Filippakopoulos, P. / Qi, J. / Picaud, S. / Shen, Y. / Smith, W.B. / Fedorov, O. / Morse, E.M. / Keates, T. / Hickman, T.T. / Felletar, I. / Philpott, M. / Munro, S. / McKeown, M.R. / Wang, Y. / Christie, A.L. / West, N. / Cameron, M.J. / Schwartz, B. / Heightman, T.D. / La Thangue, N. / French, C.A. / Wiest, O. / Kung, A.L. / Knapp, S. / Bradner, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oni.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oni.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 3oni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oni_validation.pdf.gz | 821.6 KB | Display | wwPDB validaton report |
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Full document | 3oni_full_validation.pdf.gz | 822.1 KB | Display | |
Data in XML | 3oni_validation.xml.gz | 9 KB | Display | |
Data in CIF | 3oni_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3oni ftp://data.pdbj.org/pub/pdb/validation_reports/on/3oni | HTTPS FTP |
-Related structure data
Related structure data | 3mxfC 2nxbS 2oo1S 2ossS 2ouoS 2rfjS 3d7cS 3daiS 3dwyS 3hmhS 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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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.: 1 / Fragment: residues 224-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, DKFZp313H139, hCG_17503 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q658Y7, UniProt: P25440*PLUS | ||||
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#2: Chemical | ChemComp-JQ1 / ( | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% Jeffamine600, 0.5M CsCl, 5% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 22, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.4 % / Av σ(I) over netI: 10 / Number: 54515 / Rsym value: 0.055 / D res high: 1.609 Å / D res low: 27.32 Å / Num. obs: 16213 / % possible obs: 99.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.61→29.16 Å / Num. all: 16295 / Num. obs: 16213 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 16.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 29.42 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY Resolution: 1.61→29.16 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1778 / WRfactor Rwork: 0.145 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9219 / SU B: 1.988 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0793 / SU Rfree: 0.0822 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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 max: 62.26 Å2 / Biso mean: 13.0347 Å2 / Biso min: 4.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→29.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.652 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 |
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