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Yorodumi- PDB-4bve: CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bve | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE | ||||||
Components |
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Keywords | HYDROLASE/LIGASE / HYDROLASE-LIGASE COMPLEX / THIO-INTERMEDIATE | ||||||
Function / homology | Function and homology information propionate biosynthetic process / acetate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / 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 / acetate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / 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 / NAD-dependent histone deacetylase activity / protein deacetylation / 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: 2.05 Å | ||||||
Authors | Gertz, M. / Weyand, M. / Steegborn, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism Authors: Gertz, M. / Fischer, F. / Nguyen, G.T.T. / Lakshminarasimhan, M. / Schutkowski, M. / Weyand, M. / Steegborn, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bve.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bve.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 4bve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bve ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bve | HTTPS FTP |
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-Related structure data
Related structure data | 4buzC 4bv2C 4bv3C 4bvbC 4bvfC 4bvgC 4bvhC 3gltS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 31484.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 116-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVFT3S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1805.889 Da / Num. of mol.: 1 / Fragment: RESIDUES 640-645 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NUB1, acetate-CoA ligase |
-Non-polymers , 6 types, 226 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-SO4 / |
#7: Chemical | ChemComp-EDO / |
#8: Water | ChemComp-HOH / |
-Details
Sequence details | CONSTRUCT COVERS RESIDUES 116-399 |
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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: 3 Å3/Da / Density % sol: 59.02 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2012 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→34.1 Å / Num. obs: 25087 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GLT Resolution: 2.05→34.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.224 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 20.563 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.14 Å
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