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Yorodumi- PDB-3d4b: Crystal structure of Sir2Tm in complex with Acetyl p53 peptide an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d4b | ||||||
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Title | Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+ | ||||||
Components |
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Keywords | HYDROLASE / Rossmann Fold / Cytoplasm / Metal-binding / NAD / Zinc | ||||||
Function / homology | Function and homology information protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ binding / transferase activity / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Hawse, W.F. / Hoff, K.G. / Fatkins, D. / Daines, A. / Zubkova, O.V. / Schramm, V.L. / Zheng, W. / Wolberger, C. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structural insights into intermediate steps in the Sir2 deacetylation reaction. Authors: Hawse, W.F. / Hoff, K.G. / Fatkins, D.G. / Daines, A. / Zubkova, O.V. / Schramm, V.L. / Zheng, W. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d4b.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d4b.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d4b_validation.pdf.gz | 781.5 KB | Display | wwPDB validaton report |
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Full document | 3d4b_full_validation.pdf.gz | 785 KB | Display | |
Data in XML | 3d4b_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3d4b_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/3d4b ftp://data.pdbj.org/pub/pdb/validation_reports/d4/3d4b | HTTPS FTP |
-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: 27569.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: npdA, TM_0490 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1116.357 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-DZD / |
#5: 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: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 3350, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 77.4 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.99 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 23641 / Num. obs: 23509 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 1.8→1.95 Å / Rmerge(I) obs: 0.37 / % possible all: 96.54 |
-Processing
Software |
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Refinement | Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.058 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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