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Yorodumi- PDB-3glt: Crystal Structure of Human SIRT3 with ADPR bound to the AceCS2 pe... -
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-Basic information
Entry | Database: PDB / ID: 3glt | ||||||
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Title | Crystal Structure of Human SIRT3 with ADPR bound to the AceCS2 peptide containing a thioacetyl lysine | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE REGULATOR / NAD dependent deacetylase / sirtuin / intermediate trapped structure / thioacetyl peptide / Hydrolase / Metal-binding / Mitochondrion / NAD / Polymorphism / Transit peptide / Zinc / Alternative splicing / Ligase / HYDROLASE-HYDROLASE REGULATOR COMPLEX | ||||||
Function / homology | Function and homology information propionate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / acetate biosynthetic process / positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / Ethanol oxidation ...propionate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / acetate biosynthetic process / positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / Ethanol oxidation / peptidyl-lysine deacetylation / acetyl-CoA biosynthetic process / positive regulation of superoxide dismutase activity / : / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / NAD-dependent histone deacetylase activity / Regulation of FOXO transcriptional activity by acetylation / AMP binding / 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 / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 3glt.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3glt.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 3glt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3glt_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 3glt_full_validation.pdf.gz | 472.4 KB | Display | |
Data in XML | 3glt_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3glt_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/3glt ftp://data.pdbj.org/pub/pdb/validation_reports/gl/3glt | HTTPS FTP |
-Related structure data
Related structure data | 3glrSC 3glsC 3gluC 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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.) Homo sapiens (human) / Gene: SIR2L3, SIRT3 / 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 |
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#2: Protein/peptide | Mass: 2076.241 Da / Num. of mol.: 1 / Fragment: AceCS2 peptide, residues 638-649 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NUB1, acetate-CoA ligase |
-Non-polymers , 4 types, 145 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-CO3 / |
#6: 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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 291 K / 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 |
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: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→65 Å / Num. obs: 23467 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GLR Resolution: 2.1→65 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.916 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.16 / 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: 21.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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