+Open data
-Basic information
Entry | Database: PDB / ID: 5d7n | |||||||||
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Title | Crystal structure of human Sirt3 at an improved resolution | |||||||||
Components | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | |||||||||
Keywords | HYDROLASE / Sirtuin 3 / Deacylase | |||||||||
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: 1.83 Å | |||||||||
Authors | Rumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking. Authors: Rumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d7n.cif.gz | 652.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d7n.ent.gz | 540.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/5d7n ftp://data.pdbj.org/pub/pdb/validation_reports/d7/5d7n | HTTPS FTP |
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-Related structure data
Related structure data | 5d7oC 5d7pC 5d7qC 3glsS 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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3 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 31268.049 Da / Num. of mol.: 6 / Fragment: UNP residues 118-395 Source method: isolated from a genetically manipulated source Details: Gly1 originates from TEV cleavage site His2/Met3 originate from NdeI restriction site of the vector Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 8 types, 1274 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-1PE / | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-PGE / | #8: Chemical | ChemComp-PG4 / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride, 25 % (w/v) PEG 3350 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→33.66 Å / Num. obs: 168813 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.83→1.86 Å / Rmerge(I) obs: 0.815 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GLS Resolution: 1.83→33.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.862 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.762 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→33.66 Å
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