+Open data
-Basic information
Entry | Database: PDB / ID: 5cae | ||||||
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Title | Succinate bound to pig GTP-specific succinyl-CoA synthetase | ||||||
Components | (Succinyl-CoA ligase ...) x 2 | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / GTP binding / mitochondrion / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Huang, J. / Fraser, M.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Structural basis for the binding of succinate to succinyl-CoA synthetase. Authors: Huang, J. / Fraser, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cae.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cae.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 5cae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/5cae ftp://data.pdbj.org/pub/pdb/validation_reports/ca/5cae | HTTPS FTP |
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-Related structure data
Related structure data | 4xx0S 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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Details | SDS-PAGE/Gel filtration (G100 Sephadex) confirms the heterodimer. |
-Components
-Succinyl-CoA ligase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33131.016 Da / Num. of mol.: 1 / Fragment: UNP residues 42-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O19069, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming) |
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#2: Protein | Mass: 42667.809 Da / Num. of mol.: 1 / Fragment: UNP residues 40-433 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG2 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53590, succinate-CoA ligase (GDP-forming) |
-Non-polymers , 7 types, 257 molecules
#3: Chemical | ChemComp-COA / | ||||||||
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#4: Chemical | ChemComp-CL / | ||||||||
#5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-SIN / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, ammonium succinate, magnesium chloride, CoA, HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97947 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 20, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→49.073 Å / Num. all: 33544 / Num. obs: 33544 / % possible obs: 97 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.81 Å2 / Rpim(I) all: 0.058 / Rrim(I) all: 0.113 / Rsym value: 0.096 / Net I/av σ(I): 6.964 / Net I/σ(I): 9.3 / Num. measured all: 122021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4XX0 Resolution: 2.2→49.073 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
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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 max: 84.03 Å2 / Biso mean: 30.7228 Å2 / Biso min: 13.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→49.073 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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