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- PDB-2od7: Crystal Structure of yHst2 bound to the intermediate analogue ADP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2od7 | ||||||
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Title | Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated H4 peptide | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marmorstein, R.Q. / Sanders, B.D. | ||||||
![]() | ![]() Title: Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes. Authors: Sanders, B.D. / Zhao, K. / Slama, J.T. / Marmorstein, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.5 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2od2C ![]() 2od9C ![]() 2qqfC ![]() 2qqgC ![]() 1szdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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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. |
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Components
#1: Protein | Mass: 34794.828 Da / Num. of mol.: 1 / Fragment: Hst2 catalytic core domain, residues 1-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HST2 / Plasmid: pRSET-A / Production host: ![]() ![]() ![]() References: UniProt: P53686, ![]() |
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#2: Protein/peptide | Mass: 1610.925 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-A1R / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.67 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0 M Ammonium Sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. all: 28626 / Num. obs: 28626 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.064 / Rsym value: 0.053 / Χ2: 0.983 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 27 / Num. unique all: 2847 / Rsym value: 0.342 / Χ2: 0.996 / % possible all: 94.2 |
-Phasing
Phasing MR | Rfactor: 0.423 / Cor.coef. Fo:Fc: 0.542 / Cor.coef. Io to Ic: 0.142
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1SZD Resolution: 2→41.92 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 50.945 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.558 Å2
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Refinement step | Cycle: LAST / Resolution: 2→41.92 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||
Xplor file |
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