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- PDB-5eek: 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: 5eek | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trichostatin A | ||||||
![]() | Hdac6 protein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / 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 | ![]() ![]() ![]() | ||||||
![]() | Hai, Y. / Christianson, D.W. | ||||||
![]() | ![]() Title: Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Authors: Hai, Y. / 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 | ![]() | 170.2 KB | Display | ![]() |
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PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 725.7 KB | Display | ![]() |
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Full document | ![]() | 729.4 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eduC ![]() 5eefC ![]() 5eeiSC ![]() 5eemC ![]() 5eenC ![]() 5ef7C ![]() 5ef8C ![]() 5efbC ![]() 5efgC ![]() 5efhC ![]() 5efjC ![]() 5efkC ![]() 5efnC C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40285.484 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 288-646) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A7YT55, UniProt: F8W4B7*PLUS, histone deacetylase |
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-Non-polymers , 9 types, 416 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/TSN.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/TSN.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-TSN / | #5: Chemical | ChemComp-IOD / #6: Chemical | ChemComp-NH4 / #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-GOL / | #9: Chemical | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M ammonium iodide, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28184 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. all: 56038 / Num. obs: 55924 / % possible obs: 100 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.59→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5EEI Resolution: 1.59→44.011 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→44.011 Å
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Refine LS restraints |
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LS refinement shell |
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