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Yorodumi- PDB-4hda: Crystal structure of human Sirt5 in complex with Fluor-de-Lys pep... -
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-Basic information
Entry | Database: PDB / ID: 4hda | ||||||
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Title | Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE ACTIVATOR / NAD-dependent deacetylase / Sirtuin / mitochondrial / activator complex / resveratrol / HYDROLASE-HYDROLASE ACTIVATOR complex | ||||||
Function / homology | Function and homology information protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / transferase activity / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å | ||||||
Authors | Gertz, M. / Steegborn, C. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: A molecular mechanism for direct sirtuin activation by resveratrol. Authors: Gertz, M. / Nguyen, G.T. / Fischer, F. / Suenkel, B. / Schlicker, C. / Franzel, B. / Tomaschewski, J. / Aladini, F. / Becker, C. / Wolters, D. / Steegborn, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hda.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hda.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/4hda ftp://data.pdbj.org/pub/pdb/validation_reports/hd/4hda | HTTPS FTP |
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-Related structure data
-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
#1: Protein | Mass: 29913.078 Da / Num. of mol.: 2 / Fragment: UNP residues 34-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L5, SIRT5 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2 References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | | Mass: 769.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: coumarin-modified tetra peptide #3: Chemical | #4: Chemical | ChemComp-STL / | #5: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 150 mM NH4Cl, 15% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.521 |
Reflection | Resolution: 2.6→38.8 Å / Num. all: 15731 / Num. obs: 15354 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→38.778 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8104 / σ(F): 0 / Phase error: 25.81 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.671 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.99 Å2 / Biso mean: 40.8352 Å2 / Biso min: 12.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.601→38.778 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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