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- PDB-6uo3: 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: 6uo3 | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed with AR-42 | ||||||
![]() | HDAC6 | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / Histone Deacetylase / Hydrolase-Hydrolase Inhibitor complex | ||||||
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: Structural Basis of Catalysis and Inhibition of HDAC6 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 | ![]() | 122.2 KB | Display | ![]() |
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PDB format | ![]() | 72.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 334.7 KB | Display | ![]() |
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Full document | ![]() | 334.9 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uo2C ![]() 6uo4C ![]() 6uo5C ![]() 6uo7C ![]() 6uobC ![]() 6uocC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40294.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 420 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/QCP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/QCP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-QCP / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M ammonium tartrate dibasic (pH 7.0) 20% PEG 3350 1:1 ratio protein to precipitant |
-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: Aug 2, 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: 1.09→43.0926147252 Å / Num. obs: 169488 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 9.50667468151 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.062 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.09→1.12 Å / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 2 / Num. unique obs: 16796 / CC1/2: 0.776 / Rpim(I) all: 0.445 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EEF Resolution: 1.09000122285→43.0926147252 Å / SU ML: 0.100731551156 / Cross valid method: FREE R-VALUE / σ(F): 1.33645998405 / Phase error: 19.8872764084
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2140592905 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09000122285→43.0926147252 Å
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Refine LS restraints |
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LS refinement shell |
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