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Yorodumi- PDB-7sgk: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -
+Open data
-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 | ||||||
Components | Polyamine deacetylase HDAC10 | ||||||
Keywords | HYDROLASE / Histone Deacetylase | ||||||
Function / homology | Function and homology information 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 / epigenetic regulation of gene expression / macroautophagy / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sgk.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sgk.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 7sgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sgk ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sgk | 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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Danio rerio (zebrafish) / Gene: hdac10 / Production host: Escherichia coli (E. coli) References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase |
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-Non-polymers , 6 types, 252 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å |
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: 2.2→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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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