+Open data
-Basic information
Entry | Database: PDB / ID: 1q14 | ||||||
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Title | Structure and autoregulation of the yeast Hst2 homolog of Sir2 | ||||||
Components | HST2 protein | ||||||
Keywords | HYDROLASE / histone deacetylase | ||||||
Function / homology | Function and homology information Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / NAD-dependent histone H4K16 deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ binding / transferase activity / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Zhao, K. / Chai, X. / Clements, A. / Marmorstein, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure and autoregulation of the Yeast Hst2 homolog of Sir2 Authors: Zhao, K. / Chai, X. / Clements, A. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q14.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q14.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 1q14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q14_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 1q14_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 1q14_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1q14_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q14 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q14 | 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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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -1/2x-0.866y+1, 0.866x-1/2y,z and -1/2x+0.866y+1/2, -0.866x-1/2y+2/3, z |
-Components
#1: Protein | Mass: 40378.672 Da / Num. of mol.: 1 / Fragment: histone/protein deacetylase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PROD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53686 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEg4K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2003 |
Radiation | Monochromator: 0.9 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 12776 / Num. obs: 12378 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.4 % / Rmerge(I) obs: 0.057 / Rsym value: 0.062 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.9 / Num. unique all: 1267 / Rsym value: 0.207 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 12776 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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Refinement | *PLUS Rfactor Rwork: 0.218 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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