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- PDB-7sgk: 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: 7sgk | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with DKFZ-728 | ||||||
![]() | Polyamine deacetylase HDAC10 | ||||||
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Function / homology | ![]() polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / : / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 177.3 KB | Display | ![]() |
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PDB format | ![]() | 109.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sggC ![]() 7sgiC ![]() 7sgjC ![]() 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, ![]() ![]() |
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-Non-polymers , 6 types, 252 molecules ![](data/chem/img/9A9.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/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-9A9 / | ||||||
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#3: Chemical | ChemComp-ZN / | ||||||
#4: Chemical | #5: Chemical | ![]() #6: Chemical | ChemComp-NA / | #7: 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: 3.04 Å3/Da / Density % sol: 59.49 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC10, 2 mM DKFZ-728, 1:1000 trypsin:HDAC10, 0.192 M Sodium Phosphate Monobasic, 0.008 M Sodium 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![]() |
Reflection | Resolution: 2.2→69.76 Å / Num. obs: 47515 / % possible obs: 99.8 % / Redundancy: 9.1 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.072 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4052 / CC1/2: 0.667 / Rpim(I) all: 0.653 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5TD7 Resolution: 2.2→69.76 Å / SU ML: 0.3014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7023 / 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: 48.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→69.76 Å
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Refine LS restraints |
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LS refinement shell |
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