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Yorodumi- PDB-8gqz: Crystal structure of mitochondrial citrate synthase (Cit1) from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gqz | |||||||||
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Title | Crystal structure of mitochondrial citrate synthase (Cit1) from Saccharomyces cerevisiae | |||||||||
Components | Citrate synthase | |||||||||
Keywords | TRANSFERASE / TCA cycle / mitochondrial protein / citrate metabolism / SCFUcc1 ubiquitin ligase / proteasome-dependent degradation | |||||||||
Function / homology | Function and homology information citrate (Si)-synthase activity / citrate metabolic process / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 | 8gqz.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqz.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqz ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqz | HTTPS FTP |
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-Related structure data
Related structure data | 8gr8C 8gr9C 8greC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53432.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CIT1, GI527_G0005109 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q7J3 |
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-Non-polymers , 5 types, 955 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
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: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 140 mM Ca(OAc)2, 70 mM Tris pH 7.0, 14% (w/v) PEG 3000 |
-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: Jul 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→31.64 Å / Num. obs: 173510 / % possible obs: 97.91 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 26.36 |
Reflection shell | Resolution: 1.42→1.471 Å / Num. unique obs: 16335 / CC1/2: 0.897 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→31.64 Å / SU ML: 0.1418 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3746 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 21.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→31.64 Å
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Refine LS restraints |
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LS refinement shell |
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