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Yorodumi- PDB-3uvx: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uvx | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K12acK16ac) | ||||||
Components |
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Keywords | TRANSCRIPTION/PROTEIN BINDING / Bromodomain / Bromodomain containing protein 4 / CAP / HUNK1 / MCAP / Mitotic chromosome associated protein / peptide complex / Structural Genomics Consortium / SGC / TRANSCRIPTION-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / toxin activity / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Keates, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / 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 | 3uvx.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uvx.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uvx_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 3uvx_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 3uvx_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3uvx_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/3uvx ftp://data.pdbj.org/pub/pdb/validation_reports/uv/3uvx | HTTPS FTP |
-Related structure data
Related structure data | 2nxbC 2oo1SC 2ossSC 2ouoSC 2rfjC 3d7cSC 3daiSC 3dwyC 3gg3C 3hmeC 3hmfC 3hmhC 3i3jC 3iu5C 3iu6C 3lxjC 3mb3C 3mb4C 3mqmC 3nxbC 3p1cC 3p1dC 3q2eC 3rcwC 3tlpC 3uv2C 3uv4C 3uv5C 3uvdC 3uvwC 3uvyC 3uw9C 2grcS 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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Unit cell |
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Details | Monomer |
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: unp residues 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O60885 |
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#2: Protein/peptide | Mass: 1281.511 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Human Histone 4 peptide (Uniprot: P62805) residues 11-21 acetylated on K12 and K16 Source: (synth.) homo sapiens (human) / References: UniProt: P62805*PLUS |
-Non-polymers , 4 types, 105 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: 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: 2.02 Å3/Da / Density meas: 39.23 Mg/m3 / Density % sol: 39.23 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.35M NaFortmate 20% PEG 3350 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 6, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.4 % / Av σ(I) over netI: 4.8 / Number: 47477 / Rsym value: 0.112 / D res high: 1.91 Å / D res low: 22.497 Å / Num. obs: 10804 / % possible obs: 99.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.91→24.09 Å / Num. all: 10815 / Num. obs: 10804 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 53.45 / 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 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C Resolution: 1.91→24.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.1627 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8728 / SU B: 6.294 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1569 / SU Rfree: 0.1476 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.148 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.77 Å2 / Biso mean: 27.8702 Å2 / Biso min: 11.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→24.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.959 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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