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Yorodumi- PDB-6uim: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uim | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-{[(3-aminopropyl)amino]-2-oxoheptyl} thioacetate | ||||||
Components | Polyamine deacetylase HDAC10 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Histone Deacetylase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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: 2.75 Å | ||||||
Authors | Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Binding ofN8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation. Authors: Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uim.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uim.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 6uim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/6uim ftp://data.pdbj.org/pub/pdb/validation_reports/ui/6uim | HTTPS FTP |
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-Related structure data
Related structure data | 6ufnC 6ufoC 6uhuC 6uhvC 6uiiC 6uijC 6uilC 5td7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 75041.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli) References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase |
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-Non-polymers , 5 types, 20 molecules
#2: Chemical | ChemComp-Q7Y / | ||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL zHDAC10, 5 mM inhibitor 2, 1:1000 trypsin:zHDAC10, 0.2 M potassium phosphate monobasic, 20% PEG3350, and 0.5% (w/v) n-dodecyl-B-D-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→45.73 Å / Num. obs: 24629 / % possible obs: 99.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 67.25 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.085 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.75→2.85 Å / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2416 / CC1/2: 0.842 / Rpim(I) all: 0.448 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5td7 Resolution: 2.75→45.73 Å / SU ML: 0.412 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2058
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→45.73 Å
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Refine LS restraints |
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LS refinement shell |
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