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Yorodumi- PDB-1q17: Structure of the yeast Hst2 protein deacetylase in ternary comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q17 | ||||||
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Title | Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Zhao, K. / Chai, X. / Marmorstein, R. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of the Yeast Hst2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl ADP Ribose and Histone Peptide. Authors: Zhao, K. / Chai, X. / Marmorstein, R. #1: 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 | 1q17.cif.gz | 192.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q17.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 1q17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q17_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1q17_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1q17_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 1q17_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q17 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q17 | HTTPS FTP |
-Related structure data
Related structure data | 1q1aC 1q14S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33809.730 Da / Num. of mol.: 3 / Fragment: protein deacetylase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HST2 OR YPL015C OR LPA2C / Production host: Escherichia coli (E. coli) / References: UniProt: P53686 #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.28 Å3/Da / Density % sol: 62.44 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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: CHESS / Beamline: F1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2003 |
Radiation | Monochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 35492 / Num. obs: 34976 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 10.9 / Num. unique all: 3602 / Rsym value: 0.207 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 35492 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q14 Resolution: 2.7→28.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 243397.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3895 Å2 / ksol: 0.328581 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→28.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.335 / Rfactor Rwork: 0.265 |