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Yorodumi- PDB-1m2n: Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m2n | ||||||
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Title | Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose complex | ||||||
Components | Silent Information Regulator 2 | ||||||
Keywords | GENE REGULATION / PROTEIN-LIGAND 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chang, J. / Cho, Y. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Structural basis for the NAD-dependent deacetylase mechanism of Sir2 Authors: Chang, J.H. / Kim, H.C. / Hwang, K.Y. / Lee, J.W. / Jackson, S.P. / Bell, S.D. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m2n.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m2n.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/1m2n ftp://data.pdbj.org/pub/pdb/validation_reports/m2/1m2n | 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
#1: Protein | Mass: 27430.762 Da / Num. of mol.: 2 / Mutation: D102G, F159A, R170A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 [PREP 4] / References: UniProt: O28597 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.24 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 7 Details: PEG 8000, HEPES, pH 7.0, EVAPORATION, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 22.7 Å2 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 50 Å / Num. obs: 19629 / % possible obs: 77.3 % / Num. measured all: 81444 / Rmerge(I) obs: 0.053 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 500617.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.5956 Å2 / ksol: 0.286452 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 40 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.2289 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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