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- PDB-6uii: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uii | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 5-[(3-aminopropyl)amino]pentane-1-thiol | ||||||
![]() | Polyamine deacetylase HDAC10 | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / Histone Deacetylase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior ...polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior / regulation of tubulin deacetylation / macroautophagy / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Binding ofN8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation. Authors: Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.4 KB | Display | ![]() |
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PDB format | ![]() | 101.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 632.6 KB | Display | ![]() |
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Full document | ![]() | 635.4 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ufnC ![]() 6ufoC ![]() 6uhuC ![]() 6uhvC ![]() 6uijC ![]() 6uilC ![]() 6uimC ![]() 5td7S 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75025.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase |
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-Non-polymers , 5 types, 32 molecules ![](data/chem/img/SS9.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SS9 / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #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: 3.07 Å3/Da / Density % sol: 59.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL zHDAC10, 5 mM inhibitor 6, 1:1000 trypsin:zHDAC10, 0.2 M potassium phosphate monobasic, 20% PEG3350, and 4% v/v polypropylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→69.96 Å / Num. obs: 27778 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 63.34 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.064 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.65→2.75 Å / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2710 / CC1/2: 0.639 / Rpim(I) all: 0.725 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TD7 Resolution: 2.65→69.96 Å / SU ML: 0.3464 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7852
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→69.96 Å
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Refine LS restraints |
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LS refinement shell |
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