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Yorodumi- PDB-7kuq: Crystal Structure of Danio rerio Histone Deacetylase 10 Y307F Mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kuq | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine | ||||||
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 ...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 | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2021 Title: X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. 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 | 7kuq.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kuq.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kuq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/7kuq ftp://data.pdbj.org/pub/pdb/validation_reports/ku/7kuq | HTTPS FTP |
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-Related structure data
Related structure data | 7kurC 7kusC 7kutC 7kuvC 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: 75240.820 Da / Num. of mol.: 1 / Mutation: Y307F 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, 192 molecules
#2: Chemical | ChemComp-Q9C / | ||||||
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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: 3.1 Å3/Da / Density % sol: 60.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC10, 10 mM N8-Acetylspermidine, 1:1000 trypsin:HDAC10, 0.125 M sodium phosphate dibasic, 0.075 M sodium phosphate monobasic, 20% PEG3350 (w/v), HDAC10 microseed |
-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: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→69.72 Å / Num. obs: 55699 / % possible obs: 99.74 % / Redundancy: 7.2 % / Biso Wilson estimate: 34.45 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.084 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5526 / CC1/2: 0.0617 / Rpim(I) all: 0.437 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TD7 Resolution: 2.1→60.85 Å / SU ML: 0.3043 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9892 / 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: 39.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→60.85 Å
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Refine LS restraints |
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LS refinement shell |
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