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- PDB-5eem: 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: 5eem | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 | ||||||
![]() | Hdac6 protein | ||||||
![]() | HYDROLASE | ||||||
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 / epigenetic regulation of gene expression / 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 | ![]() | 286.9 KB | Display | ![]() |
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PDB format | ![]() | 230.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eduC ![]() 5eefC ![]() 5eeiC ![]() 5eekSC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 40285.484 Da / Num. of mol.: 2 / 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 , 5 types, 315 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate, 0.1 M sodium formate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 47957 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.8 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5EEK Resolution: 2→15.91 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.19 / 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: 2→15.91 Å
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Refine LS restraints |
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LS refinement shell |
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