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- PDB-6wyo: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wyo | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) H82F F202Y double mutant complexed with Trichostatin A | ||||||
![]() | Histone deacetylase 6 | ||||||
![]() | HYDROLASE / Histone Deacetylase / metalloprotein | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.2 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 849.7 KB | Display | ![]() |
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Full document | ![]() | 853.2 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 36.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wypC ![]() 6wyqC ![]() 5eefS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 42077.652 Da / Num. of mol.: 2 / Mutation: H82F,F202Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC6 Protein 0.2 M Potassium acetate 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50.1 Å / Num. obs: 28350 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.5564079678 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.052 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.418 / Num. unique obs: 2842 / CC1/2: 0.792 / Rpim(I) all: 0.395 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 5EEF Resolution: 2.30000278768→50.090196779 Å / SU ML: 0.29965551381 / Cross valid method: FREE R-VALUE / σ(F): 1.38501881023 / Phase error: 24.0334206853 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: 33.0078730162 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.30000278768→50.090196779 Å
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Refine LS restraints |
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LS refinement shell |
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