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- PDB-5wgi: Ultrahigh resolution crystal structure of Danio rerio histone dea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wgi | ||||||
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Title | Ultrahigh resolution crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with TSA | ||||||
![]() | Hdac6 protein![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() | ||||||
Function / homology | ![]() Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Porter, N.J. / Christianson, D.W. | ||||||
![]() | ![]() Title: Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors. Authors: Porter, N.J. / Mahendran, A. / Breslow, R. / 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 | ![]() | 252.7 KB | Display | ![]() |
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PDB format | ![]() | 204 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wgkC ![]() 5wglC ![]() 5wgmC ![]() 5eemS 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: 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.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 9 types, 446 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/TSN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TSN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||||||
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#3: Chemical | ChemComp-TSN / ![]() | ||||||||||||
#4: Chemical | #5: Chemical | ![]() #6: Chemical | ChemComp-EDO / ![]() #7: Chemical | ![]() #8: Chemical | ![]() #9: Chemical | ChemComp-MG / | #10: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, Bis-Tris, pH 6.5, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.05→47.04 Å / Num. obs: 138710 / % possible obs: 95.6 % / Redundancy: 3.3 % / Net I/σ(I): 11.1 |
Reflection shell | Highest resolution: 1.05 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 5EEM Resolution: 1.05→47.038 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→47.038 Å
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Refine LS restraints |
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LS refinement shell |
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