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Yorodumi- PDB-7jkx: Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jkx | ||||||
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Title | Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-6 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / Pan BDs Inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Amanitin/phalloidin toxin / toxin activity / Chem-Y36 / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Ratia, K.M. / Xiong, R. / Li, Y. / Shen, Z. / Zhao, J. / Huang, F. / Dubrovyskyii, O. / Thatcher, G.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-6 Authors: Xiong, R. / Ratia, K.M. / Li, Y. / Shen, Z. / Zhao, J. / Huang, F. / Dubrovyskyii, O. / Thatcher, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jkx.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jkx.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 7jkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jkx_validation.pdf.gz | 856.2 KB | Display | wwPDB validaton report |
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Full document | 7jkx_full_validation.pdf.gz | 856.7 KB | Display | |
Data in XML | 7jkx_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7jkx_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/7jkx ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jkx | HTTPS FTP |
-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: 15123.376 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 BL21(DE3) (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-Y36 / |
#3: 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: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M LiSO4, 0.1M Tris-HCl pH 8.5, 16-20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.53 Å / Num. obs: 43497 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Rrim(I) all: 0.039 / Net I/av σ(I): 28.5 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 2082 / CC1/2: 0.987 / Rpim(I) all: 0.082 / Rrim(I) all: 0.21 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXF Resolution: 1.2→19.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.617 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 52.29 Å2 / Biso mean: 14.336 Å2 / Biso min: 7.77 Å2
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Refinement step | Cycle: final / Resolution: 1.2→19.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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