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Yorodumi- PDB-4j0s: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j0s | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | SIGNALING PROTEIN / BRD4 / Bromodomain containing protein 4 / CAP / HUNK1 / MCAP / Mitotic chromosome associated protein / Isoxazole / Structural Genomics Consortium / SGC | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-1H3 / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Qi, J. / Felletar, I. / Hewings, D.S. / von Delft, F. / Conway, S.J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. ...Filippakopoulos, P. / Picaud, S. / Qi, J. / Felletar, I. / Hewings, D.S. / von Delft, F. / Conway, S.J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands. Authors: Hewings, D.S. / Fedorov, O. / Filippakopoulos, P. / Martin, S. / Picaud, S. / Tumber, A. / Wells, C. / Olcina, M.M. / Freeman, K. / Gill, A. / Ritchie, A.J. / Sheppard, D.W. / Russell, A.J. ...Authors: Hewings, D.S. / Fedorov, O. / Filippakopoulos, P. / Martin, S. / Picaud, S. / Tumber, A. / Wells, C. / Olcina, M.M. / Freeman, K. / Gill, A. / Ritchie, A.J. / Sheppard, D.W. / Russell, A.J. / Hammond, E.M. / Knapp, S. / Brennan, P.E. / Conway, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j0s.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j0s.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 4j0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j0s_validation.pdf.gz | 789 KB | Display | wwPDB validaton report |
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Full document | 4j0s_full_validation.pdf.gz | 789 KB | Display | |
Data in XML | 4j0s_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4j0s_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/4j0s ftp://data.pdbj.org/pub/pdb/validation_reports/j0/4j0s | HTTPS FTP |
-Related structure data
Related structure data | 4j0rC 2ossS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#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: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-1H3 / | #4: 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: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Na/KPO4, 20% PEG 3350, 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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 17, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.6 % / Av σ(I) over netI: 4.7 / Number: 55318 / Rsym value: 0.16 / D res high: 1.84 Å / D res low: 19.489 Å / Num. obs: 11949 / % possible obs: 99.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.84→19.49 Å / Num. all: 12045 / Num. obs: 11949 / % possible obs: 99.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 2OSS Resolution: 1.84→19.49 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.1396 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8803 / SU B: 5.426 / SU ML: 0.091 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.1408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.141 / 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: 107.33 Å2 / Biso mean: 17.0535 Å2 / Biso min: 5.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→19.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.887 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 31.2408 Å / Origin y: 25.0549 Å / Origin z: 9.3155 Å
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