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- PDB-7sgj: 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: 7sgj | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with DKFZ-711 | ||||||
![]() | Polyamine deacetylase HDAC10 | ||||||
![]() | HYDROLASE / Histone Deacetylase | ||||||
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: Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout. Authors: Steimbach, R.R. / Herbst-Gervasoni, C.J. / Lechner, S. / Stewart, T.M. / Klinke, G. / Ridinger, J. / Geraldy, M.N.E. / Tihanyi, G. / Foley, J.R. / Uhrig, U. / Kuster, B. / Poschet, G. / ...Authors: Steimbach, R.R. / Herbst-Gervasoni, C.J. / Lechner, S. / Stewart, T.M. / Klinke, G. / Ridinger, J. / Geraldy, M.N.E. / Tihanyi, G. / Foley, J.R. / Uhrig, U. / Kuster, B. / Poschet, G. / Casero Jr., R.A. / Medard, G. / Oehme, I. / Christianson, D.W. / Gunkel, N. / Miller, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.4 KB | Display | ![]() |
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PDB format | ![]() | 110.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 692.4 KB | Display | ![]() |
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Full document | ![]() | 694.1 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 37.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sggC ![]() 7sgiC ![]() 7sgkC ![]() 5td7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 75055.641 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 , 8 types, 258 molecules ![](data/chem/img/9BI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-9BI / | ||||||
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#3: Chemical | ChemComp-EDO / | ||||||
#4: Chemical | ChemComp-PEG / | ||||||
#5: Chemical | ChemComp-ZN / | ||||||
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-NA / | #9: 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: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC10, 2 mM DKFZ-711, 1:1000 trypsin:HDAC10, 0.100 M Potassium Phosphate Monobasic, 0.100 M Potassium Phosphate Dibasic, and 20% (w/v) PEG3350 |
-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: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→69.84 Å / Num. obs: 51724 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 40.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.05 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.15→2.21 Å / Rmerge(I) obs: 1.119 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4111 / CC1/2: 0.639 / Rpim(I) all: 0.569 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TD7 Resolution: 2.15→69.64 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0764 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→69.64 Å
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Refine LS restraints |
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LS refinement shell |
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