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- PDB-6dvl: 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: 6dvl | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115 | ||||||
![]() | Hdac6 protein![]() | ||||||
![]() | hydrolase/hydrolase inhibitor / histone deacetylaase / metallohydrolase / hydrolase-hydrolase inhibitor complex | ||||||
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. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. Authors: Porter, N.J. / Osko, J.D. / Diedrich, D. / Kurz, T. / Hooker, J.M. / Hansen, F.K. / 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 | ![]() | 164.8 KB | Display | ![]() |
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PDB format | ![]() | 125.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dvmC ![]() 6dvnC ![]() 6dvoC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 40285.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 400 mM NaF; 15% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→60.21 Å / Num. obs: 45551 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.967 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.142 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 1.266 / CC1/2: 0.545 / Rpim(I) all: 0.735 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5EEM Resolution: 2.1→60.206 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→60.206 Å
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Refine LS restraints |
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LS refinement shell |
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