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Yorodumi- PDB-6wyp: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wyp | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with SAHA-BPyne | ||||||
Components | Histone deacetylase 6 | ||||||
Keywords | HYDROLASE / Histone Deacetylase / metalloprotein | ||||||
Function / homology | Function and homology information Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / zinc ion binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40006356531 Å | ||||||
Authors | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6. Authors: Osko, J.D. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wyp.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wyp.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 6wyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wyp_validation.pdf.gz | 819.1 KB | Display | wwPDB validaton report |
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Full document | 6wyp_full_validation.pdf.gz | 825.1 KB | Display | |
Data in XML | 6wyp_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6wyp_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/6wyp ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wyp | HTTPS FTP |
-Related structure data
Related structure data | 6wyoC 6wyqC 5eefS 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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-Components
#1: Protein | Mass: 42036.602 Da / Num. of mol.: 1 / Mutation: K330L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7 | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-UFS / | #5: 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: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC6 Protein 0.2 M Potassium Sodium Tartrate Tetrahydrate 20% PEG 3350 1:1 ratio protein to precipitant solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→54.26 Å / Num. obs: 15104 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.9586092758 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.119 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 0.817 / Num. unique obs: 1483 / CC1/2: 0.618 / Rpim(I) all: 0.507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 5EEF Resolution: 2.40006356531→54.25087491 Å / SU ML: 0.249125312227 / Cross valid method: FREE R-VALUE / σ(F): 1.33784508885 / Phase error: 25.3867738361 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.1448075816 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.40006356531→54.25087491 Å
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Refine LS restraints |
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LS refinement shell |
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