+Open data
-Basic information
Entry | Database: PDB / ID: 5uqs | ||||||
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Title | Crystal structure of Citrate synthase from Sus scrofa | ||||||
Components | Citrate synthase, mitochondrial | ||||||
Keywords | TRANSFERASE / porcine citrate synthase | ||||||
Function / homology | Function and homology information citrate (Si)-synthase / Maturation of TCA enzymes and regulation of TCA cycle / citrate synthase activity / Citric acid cycle (TCA cycle) / citrate (Si)-synthase activity / citrate metabolic process / Mitochondrial protein degradation / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Schlachter, C. / Chruszcz, M. | ||||||
Citation | Journal: Biol.Chem. / Year: 2019 Title: Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase. Authors: Schlachter, C.R. / Klapper, V. / Radford, T. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uqs.cif.gz | 367.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uqs.ent.gz | 296.8 KB | Display | PDB format |
PDBx/mmJSON format | 5uqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/5uqs ftp://data.pdbj.org/pub/pdb/validation_reports/uq/5uqs | HTTPS FTP |
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-Related structure data
Related structure data | 5uqoC 5uqqC 5uqrC 5uquC 5uzpC 5uzqC 5uzrC 6bolC 6bomC 6bonC 6booC 6bopC 3enjS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 31 - 462 / Label seq-ID: 31 - 462
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-Components
#1: Protein | Mass: 51691.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00889, citrate (Si)-synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 NaTartrate pH 7.85, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50.01 Å / Num. obs: 104042 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.046 / Rrim(I) all: 0.068 / Rsym value: 0.061 / Net I/σ(I): 19.95 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 5428 / CC1/2: 0.733 / Rpim(I) all: 0.359 / Rrim(I) all: 0.53 / Rsym value: 0.344 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ENJ Resolution: 1.6→34 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.081 / 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: 21.29 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→34 Å
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Refine LS restraints |
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