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Yorodumi- PDB-6zed: CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zed | ||||||
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Title | CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F1 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | CELL CYCLE / BROMODOMAIN-CONTAINING PROTEIN 4 ISOFORM LONG / BRD4 / BROMODOMAIN-CONTAINING PROTEIN 4 / CAP / HUNK1 / MCAP / MITOTIC CHROMOSOME ASSOCIATED PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Amanitin/phalloidin toxin / toxin activity / Chem-QGN / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å | ||||||
Authors | Krojer, T. / Martinez-Cartro, M. / Picaud, S. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Barril, X. / von Delft, F. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F1 Authors: Martinez-Cartro, M. / Barril, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zed.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zed.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/6zed ftp://data.pdbj.org/pub/pdb/validation_reports/ze/6zed | HTTPS FTP |
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-Related structure data
Related structure data | 3mxfS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 | ||||
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#2: Chemical | ChemComp-QGN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M bis-tris-propane pH 6.5, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→38.353 Å / Num. obs: 52386 / % possible obs: 92.9 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.08→1.1 Å / Num. unique obs: 2148 / CC1/2: 0.981 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3MXF Resolution: 1.08→38.352 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.655 / SU ML: 0.015 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.386 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→38.352 Å
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Refine LS restraints |
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LS refinement shell |
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