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Yorodumi- PDB-5ojo: Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ojo | ||||||
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Title | Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglutaryl-CPS1 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Sirtuin / Sirt5 / Deacylase / Mitochondria | ||||||
Function / homology | Function and homology information carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process / modified amino acid binding / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / midgut development / homocysteine metabolic process / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / NAD-dependent histone deacetylase activity / cellular response to fibroblast growth factor stimulus / response to growth hormone / response to food / glutamate binding / nitric oxide metabolic process / response to zinc ion / heterocyclic compound binding / glutamine metabolic process / response to dexamethasone / cellular response to glucagon stimulus / response to starvation / mitochondrial nucleoid / response to amine / small molecule binding / potassium ion binding / acyl binding / NAD+ binding / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to cAMP / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / vasodilation / response to toxic substance / phospholipid binding / endopeptidase activity / transferase activity / response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / mitochondrion / zinc ion binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 | 5ojo.cif.gz | 228.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ojo.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ojo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ojo_validation.pdf.gz | 484.1 KB | Display | wwPDB validaton report |
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Full document | 5ojo_full_validation.pdf.gz | 487.2 KB | Display | |
Data in XML | 5ojo_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 5ojo_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojo ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojo | HTTPS FTP |
-Related structure data
Related structure data | 5oj7C 5ojnC 4utvS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 34 - 298 / Label seq-ID: 11 - 275
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 30423.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: sirt5, si:ch211-121a2.1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6DHI5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | | Mass: 1112.230 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: N-terminal benzoylated glycine. HMG-modified lysine Source: (synth.) Homo sapiens (human) References: UniProt: P31327, carbamoyl-phosphate synthase (ammonia) |
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-Non-polymers , 6 types, 65 molecules
#3: Chemical | ChemComp-DMS / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-EPE / | #7: Chemical | ChemComp-NA / | #8: 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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: rod-shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES pH 7.6 20% PEG3350 / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 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: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 13919 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.248 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1214 / CC1/2: 0.598 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UTV Resolution: 3.1→48.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.877 / SU B: 45.042 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / 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: 71.83 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→48.67 Å
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Refine LS restraints |
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