+Open data
-Basic information
Entry | Database: PDB / ID: 1yc2 | ||||||
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Title | Sir2Af2-NAD-ADPribose-nicotinamide | ||||||
Components | NAD-dependent deacetylase 2 | ||||||
Keywords | HYDROLASE / sir2 / sirtuin / nicotinamide / NAD / ADPribose / ternary complex | ||||||
Function / homology | Function and homology information protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD+ binding / transferase activity / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Avalos, J.L. / Bever, M.K. / Wolberger, C. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme. Authors: Avalos, J.L. / Bever, K.M. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yc2.cif.gz | 269.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yc2.ent.gz | 216.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1yc2 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1yc2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 28537.006 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: npdA2 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS References: UniProt: O30124, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 10 types, 287 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-NCA / #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-PGE / | #10: Chemical | ChemComp-APR / | #11: 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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: HEPES, ammonium sulfate, PEG400, nicotinamide, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.099997 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003 |
Radiation | Monochromator: 2 CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.099997 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 59851 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.108 / Rsym value: 0.086 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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