+Open data
-Basic information
Entry | Database: PDB / ID: 7p6y | ||||||
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Title | N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 5ef | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST | ||||||
Function / homology | Amanitin/phalloidin toxin / toxin activity / Chem-5Z1 / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å | ||||||
Authors | Chung, C. | ||||||
Citation | Journal: Chemistry / Year: 2021 Title: One-Step Synthesis of Photoaffinity Probes for Live-Cell MS-Based Proteomics. Authors: Fallon, D.J. / Lehmann, S. / Chung, C.W. / Phillipou, A. / Eberl, C. / Fantom, K.G.M. / Zappacosta, F. / Patel, V.K. / Bantscheff, M. / Schofield, C.J. / Tomkinson, N.C.O. / Bush, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p6y.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p6y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p6y_validation.pdf.gz | 918.4 KB | Display | wwPDB validaton report |
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Full document | 7p6y_full_validation.pdf.gz | 920.9 KB | Display | |
Data in XML | 7p6y_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7p6y_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/7p6y ftp://data.pdbj.org/pub/pdb/validation_reports/p6/7p6y | HTTPS FTP |
-Related 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
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.18 Å3/Da / Density % sol: 43.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 sodium citrate pH 5.6, 10% w/v PEG4K, 10% w/v propan-2-ol |
-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: 0.97951 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2017 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.88→59.96 Å / Num. obs: 20355 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8 | ||||||||||||||||||
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1034 / CC1/2: 0.839 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house model Resolution: 1.881→59.957 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.996 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.032 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.513 Å2
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Refinement step | Cycle: LAST / Resolution: 1.881→59.957 Å
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Refine LS restraints |
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LS refinement shell |
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