+Open data
-Basic information
Entry | Database: PDB / ID: 4fvt | ||||||
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Title | Human SIRT3 bound to Ac-ACS peptide and Carba-NAD | ||||||
Components |
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Keywords | HYDROLASE / Sirtuin / Carba-NAD | ||||||
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 / 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 / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||
Authors | Dai, H. | ||||||
Citation | Journal: J.Org.Chem. / Year: 2012 Title: Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5. Authors: Szczepankiewicz, B.G. / Dai, H. / Koppetsch, K.J. / Qian, D. / Jiang, F. / Mao, C. / 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 | 4fvt.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fvt.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/4fvt ftp://data.pdbj.org/pub/pdb/validation_reports/fv/4fvt | HTTPS FTP |
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-Related 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: 30553.260 Da / Num. of mol.: 1 / Fragment: UNP residues 122-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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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#2: Protein/peptide | Mass: 544.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Ac-ACS2 peptide |
-Non-polymers , 5 types, 61 molecules
#3: Chemical | ChemComp-CNA / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-GOL / | #7: 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: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.2M lithium sulfate monohydrate, 15% (w/v) poly-ethylene glycol (PEG) 12000, and 0.1 M Bis-Tris, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97849 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→38.72 Å / Num. all: 13699 / Num. obs: 13699 / % possible obs: 99.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 3.6 |
Reflection shell | Resolution: 2.47→2.53 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→38.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.257 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.762 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→38.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.47→2.534 Å / Total num. of bins used: 20
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