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Yorodumi- PDB-5ojn: Sirtuin 4 from Xenopus tropicalis in complex with thioacetyl-ADP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ojn | ||||||
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Title | Sirtuin 4 from Xenopus tropicalis in complex with thioacetyl-ADP-ribose | ||||||
Components | NAD-dependent protein deacylase | ||||||
Keywords | SIGNALING PROTEIN / Sirtuin / Sirt4 / Deacylase / Mitochondria | ||||||
Function / homology | Function and homology information NAD-dependent protein lysine deacetylase activity / protein deacetylation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / mitochondrial matrix / zinc ion binding Similarity search - Function | ||||||
Biological species | Xenopus tropicalis (tropical clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pannek, M. / Steegborn, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features. Authors: Pannek, M. / Simic, Z. / Fuszard, M. / Meleshin, M. / Rotili, D. / Mai, A. / Schutkowski, M. / Steegborn, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ojn.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ojn.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ojn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ojn_validation.pdf.gz | 703.5 KB | Display | wwPDB validaton report |
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Full document | 5ojn_full_validation.pdf.gz | 708.3 KB | Display | |
Data in XML | 5ojn_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5ojn_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojn ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojn | HTTPS FTP |
-Related structure data
Related structure data | 5oj7SC 5ojoC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32100.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: sirt4, TGas015j14.1-001 / Production host: Escherichia coli (E. coli) References: UniProt: Q28CB4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-9X8 / |
#4: 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: 2.2 Å3/Da / Density % sol: 44.4 % / Description: Diamonds |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.5 M Na/K-tartrate 0.5% PEG5000MME 0.1 M Tris / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2015 / Details: Sagitally bended Si111-crystal |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 26585 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1932 / CC1/2: 0.704 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OJ7 Resolution: 1.8→19.74 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.45 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.118 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.417 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→19.74 Å
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Refine LS restraints |
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