+Open data
-Basic information
Entry | Database: PDB / ID: 5j8j | ||||||
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Title | A histone deacetylase from Saccharomyces cerevisiae | ||||||
Components | Histone deacetylase HDA1 | ||||||
Keywords | HYDROLASE / Rossmann fold / deacetylase | ||||||
Function / homology | Function and homology information HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / histone deacetylase / SUMOylation of chromatin organization proteins / histone deacetylase activity / histone deacetylase complex / chromatin binding / negative regulation of transcription by RNA polymerase II ...HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / histone deacetylase / SUMOylation of chromatin organization proteins / histone deacetylase activity / histone deacetylase complex / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.716 Å | ||||||
Authors | Zhu, Y. / Shen, H. / Li, X. / Teng, M. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae. Authors: Shen, H. / Zhu, Y. / Wang, C. / Yan, H. / Teng, M. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j8j.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j8j.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 5j8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j8j_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 5j8j_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 5j8j_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5j8j_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/5j8j ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j8j | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 28885.723 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 457-698 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HDA1, YNL021W, N2819 / Production host: Escherichia coli (E. coli) / References: UniProt: P53973, histone deacetylase |
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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: 4.79 Å3/Da / Density % sol: 74.31 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9792 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Mar 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 14972 / % possible obs: 98.1 % / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.7 |
Reflection shell | Redundancy: 10.3 % / Mean I/σ(I) obs: 3.1 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.716→40.284 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.716→40.284 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -46.2438 Å / Origin y: 18.2399 Å / Origin z: -25.4993 Å
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Refinement TLS group | Selection details: all |