+Open data
-Basic information
Entry | Database: PDB / ID: 7wjl | |||||||||||||||
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Title | Crystal structure of S. cerevisiae Hos3 | |||||||||||||||
Components | Histone deacetylase HOS3 | |||||||||||||||
Keywords | HYDROLASE / fungal histone deacetylase / Hos3 | |||||||||||||||
Function / homology | ACETATE ION / : Function and homology information | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | |||||||||||||||
Authors | Pang, N.N. / Che, S.Y. / Yang, N. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Structural characterization of fungus-specific histone deacetylase Hos3 provides insights into developing selective inhibitors with antifungal activity. Authors: Pang, N. / Sun, J. / Che, S. / Yang, N. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wjl.cif.gz | 199.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wjl.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/7wjl ftp://data.pdbj.org/pub/pdb/validation_reports/wj/7wjl | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53684.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SCNYR20_0005014500, SCP684_0005014800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6V8S402 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.05 M HEPES 7.0, 0.1 M ammonium acetate, 0.02 M magnesium chloride, 8% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97893 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 25383 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 55.02 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 1239 / CC1/2: 0.952 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→39.38 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.87 / Stereochemistry target values: ML
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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 max: 103.21 Å2 / Biso mean: 40.3311 Å2 / Biso min: 18.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→39.38 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 7.7321 Å / Origin y: 83.2109 Å / Origin z: 34.1105 Å
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Refinement TLS group |
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