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Yorodumi- PDB-9cbt: Crystal structure of human sirtuin 3 fragment (residues 118-399) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cbt | |||||||||||||||
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Title | Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10 | |||||||||||||||
Components | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | |||||||||||||||
Keywords | HYDROLASE / Deacetylase | |||||||||||||||
Function / homology | Function and homology information positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / 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 / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / aerobic respiration / 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 / molecular replacement / Resolution: 1.95 Å | |||||||||||||||
Authors | Fenwick, M.K. / Young, H.J. / Lin, H. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To Be Published Title: Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10 Authors: Fenwick, M.K. / Young, J.H. / Lin, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cbt.cif.gz | 246 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cbt.ent.gz | 194.1 KB | Display | PDB format |
PDBx/mmJSON format | 9cbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cbt_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 9cbt_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 9cbt_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 9cbt_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/9cbt ftp://data.pdbj.org/pub/pdb/validation_reports/cb/9cbt | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31340.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9NTG7 |
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-Non-polymers , 5 types, 363 molecules
#2: Chemical | #3: Chemical | ChemComp-5IA / | Mass: 1175.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H86N9O16P2S / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-5I7 / ( | Mass: 1175.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H86N9O16P2S / Feature type: SUBJECT OF INVESTIGATION #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris, pH 7.9, 100 mM MgCl2, 20 % w/v PEG8000, and 17.5 % w/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→39.43 Å / Num. obs: 40149 / % possible obs: 97.4 % / Redundancy: 3 % / Biso Wilson estimate: 35.08 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.067 / Rrim(I) all: 0.121 / Net I/σ(I): 5.3 / Num. measured all: 119067 / Scaling rejects: 66 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.886 / Num. measured all: 8478 / Num. unique obs: 2834 / CC1/2: 0.663 / Rpim(I) all: 0.588 / Rrim(I) all: 1.068 / Net I/σ(I) obs: 1 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.43 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.85 Å2 / Biso mean: 47.5708 Å2 / Biso min: 21.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→39.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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