+Open data
-Basic information
Entry | Database: PDB / ID: 3gls | ||||||
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Title | Crystal Structure of Human SIRT3 | ||||||
Components | NAD-dependent deacetylase sirtuin-3, mitochondrial | ||||||
Keywords | HYDROLASE / NAD dependent deacetylase / sirtuin / apo structure / Metal-binding / Mitochondrion / NAD / Polymorphism / Transit peptide / Zinc | ||||||
Function / homology | Function and homology information positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gls.cif.gz | 321 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gls.ent.gz | 262.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/3gls ftp://data.pdbj.org/pub/pdb/validation_reports/gl/3gls | HTTPS FTP |
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-Related structure data
Related structure data | 3glrSC 3gltC 3gluC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 31612.348 Da / Num. of mol.: 6 / Fragment: Human SIRT3, residues 118-399 / Mutation: residues 118-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Plasmid: modified pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #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: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 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: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→65 Å / Num. obs: 45823 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6877 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GLR Resolution: 2.7→65 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.172 / SU ML: 0.247 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.317 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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