+Open data
-Basic information
Entry | Database: PDB / ID: 5uzq | ||||||
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Title | Crystal structure of citrate synthase from homo sapiens | ||||||
Components | Citrate synthase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information citrate (Si)-synthase / citrate (Si)-synthase activity / Citric acid cycle (TCA cycle) / citrate metabolic process / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / carbohydrate metabolic process / mitochondrial matrix ...citrate (Si)-synthase / citrate (Si)-synthase activity / Citric acid cycle (TCA cycle) / citrate metabolic process / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 | 5uzq.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uzq.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/5uzq ftp://data.pdbj.org/pub/pdb/validation_reports/uz/5uzq | HTTPS FTP |
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-Related structure data
Related structure data | 5uqoC 5uqqC 5uqrC 5uqsC 5uquC 5uzpC 5uzrC 6bolC 6bomC 6bonC 6booC 6bopC C: citing same article (ref.) |
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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: 51889.086 Da / Num. of mol.: 1 / Fragment: residues 15-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CS / Production host: Escherichia coli (E. coli) / References: UniProt: B4DJV2, UniProt: O75390*PLUS |
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#2: 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: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 0.1 M Succinic Acid pH 7.0, 12% 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: Aug 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50.01 Å / Num. obs: 29021 / % possible obs: 93.01 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Rsym value: 0.068 / Net I/σ(I): 25.87 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 1500 / CC1/2: 0.968 / Rpim(I) all: 0.148 / Rrim(I) all: 0.483 / Rsym value: 0.323 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.184 / 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: 52.369 Å2
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Refinement step | Cycle: 1 / Resolution: 2.16→50.01 Å
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Refine LS restraints |
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