+Open data
-Basic information
Entry | Database: PDB / ID: 8gre | |||||||||
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Title | F-box protein in complex with skp1(FL) and substrate | |||||||||
Components |
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Keywords | TRANSFERASE/LIGASE / F-box protein / glyoxylate cycle / E3 ubiquitin ligase / LIGASE / TRANSFERASE-LIGASE complex | |||||||||
Function / homology | Function and homology information citrate (Si)-synthase activity / citrate metabolic process / tricarboxylic acid cycle / ubiquitin-dependent protein catabolic process / protein ubiquitination / carbohydrate metabolic process / mitochondrial matrix Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Nishio, K. / Nakatsukasa, K. / Kamura, T. / Mizushima, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Adv / Year: 2023 Title: Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Authors: Nishio, K. / Kawarasaki, T. / Sugiura, Y. / Matsumoto, S. / Konoshima, A. / Takano, Y. / Hayashi, M. / Okumura, F. / Kamura, T. / Mizushima, T. / Nakatsukasa, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gre.cif.gz | 339.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gre.ent.gz | 219.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/8gre ftp://data.pdbj.org/pub/pdb/validation_reports/gr/8gre | HTTPS FTP |
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-Related structure data
Related structure data | 8gqzC 8gr8C 8gr9C 8grfC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51476.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CIT2, GI527_G0000583 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q445 #2: Protein | | Mass: 42828.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: W303-1a / Production host: Escherichia coli (E. coli) #3: Protein | | Mass: 22357.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SKP1, GI527_G0001262 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q435 #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.79 Å3/Da / Density % sol: 55.93 % Description: The entry contains friedel pairs in I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 200 mM Na acetate, 100 mM Na citrate pH 5.5, 10% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.71 Å / Num. obs: 84031 / % possible obs: 99.63 % / Redundancy: 5.3 % / Biso Wilson estimate: 39.95 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.3→2.382 Å / Mean I/σ(I) obs: 3.28 / Num. unique obs: 8307 / CC1/2: 0.772 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.71 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8254 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The entry contains friedel pairs in I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→37.71 Å
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Refine LS restraints |
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LS refinement shell |
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