+Open data
-Basic information
Entry | Database: PDB / ID: 6wcv | ||||||
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Title | Tartryl-CoA bound to human GTP-specific succinyl-CoA synthetase | ||||||
Components |
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Keywords | LIGASE / Complex | ||||||
Function / homology | Function and homology information succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate metabolic process / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / succinyl-CoA catabolic process ...succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate metabolic process / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / succinyl-CoA catabolic process / Citric acid cycle (TCA cycle) / tricarboxylic acid cycle / Mitochondrial protein degradation / GDP binding / mitochondrial matrix / nucleotide binding / protein-containing complex binding / GTP binding / magnesium ion binding / mitochondrion / RNA binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Huang, J. / Fraser, M.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Tartryl-CoA inhibits 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 | 6wcv.cif.gz | 279 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wcv.ent.gz | 224.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wcv ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wcv | HTTPS FTP |
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-Related structure data
Related structure data | 5caeS 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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-Components
#1: Protein | Mass: 33527.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P53597, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming) |
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#2: Protein | Mass: 42627.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q96I99, succinate-CoA ligase (GDP-forming) |
#3: Chemical | ChemComp-TUY / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 17.5% (w/v) polyethylene glycol 3350, 180 mM ammonium tartrate pH 7.0, 100 mM MES pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2020 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.52→59.15 Å / Num. obs: 104120 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.4 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CAE Resolution: 1.52→59.15 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.6 / 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: 127.9 Å2 / Biso mean: 25.0089 Å2 / Biso min: 9.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→59.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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