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Open data
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Basic information
Entry | Database: PDB / ID: 3glu | ||||||
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Title | Crystal Structure of Human SIRT3 with AceCS2 peptide | ||||||
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![]() | HYDROLASE/HYDROLASE REGULATOR / NAD dependent deacetylase / ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() propionate biosynthetic process / acetate biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, L. / Wei, W. / Jiang, Y. / Peng, H. / Cai, J. / Mao, C. / Dai, H. / Bemis, J.E. / Jirousek, M.R. / Milne, J.C. ...Jin, L. / Wei, W. / Jiang, Y. / Peng, H. / Cai, J. / Mao, C. / Dai, H. / Bemis, J.E. / Jirousek, M.R. / Milne, J.C. / Westphal, C.H. / Perni, R.B. | ||||||
![]() | ![]() Title: Crystal Structures of Human SIRT3 Displaying Substrate-induced Conformational Changes. Authors: Jin, L. / Wei, W. / Jiang, Y. / Peng, H. / Cai, J. / Mao, C. / Dai, H. / Choy, W. / Bemis, J.E. / Jirousek, M.R. / Milne, J.C. / Westphal, C.H. / Perni, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.1 KB | Display | ![]() |
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PDB format | ![]() | 50.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3glrSC ![]() 3glsC ![]() 3gltC 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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Unit cell |
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Components
#1: Protein | Mass: 31612.348 Da / Num. of mol.: 1 / Fragment: Human SIRT3, residues 118-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9NTG7, ![]() | ||||
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#2: Protein/peptide | Mass: 1477.846 Da / Num. of mol.: 1 / Fragment: Human Acyl-CoA, residues 638-649 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() | ||||
#3: Chemical | ![]() #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.71 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M lithium sulfate monohydrate, 17% w/v PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2008 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→65 Å / Num. obs: 13322 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1942 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3GLR Resolution: 2.5→65 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.224 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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