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- PDB-7msr: Human E105Qa GTP-specific succinyl-CoA synthetase complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7msr | ||||||
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Title | Human E105Qa GTP-specific succinyl-CoA synthetase complexed with succinyl-phosphate, magnesium ion and desulfo-coenzyme A | ||||||
![]() | (Succinate--CoA ligase ...) x 2 | ||||||
![]() | LIGASE / Complex | ||||||
Function / homology | ![]() 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 / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, J. / Fraser, M.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase Authors: Huang, J. / Fraser, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.9 KB | Display | ![]() |
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PDB format | ![]() | 221.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.7 KB | Display | ![]() |
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Full document | ![]() | 1010.1 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 41.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mssC ![]() 7mstC ![]() 6xruS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Succinate--CoA ligase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33526.363 Da / Num. of mol.: 1 / Mutation: E105Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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.) ![]() ![]() ![]() References: UniProt: Q96I99, succinate-CoA ligase (GDP-forming) |
-Non-polymers , 6 types, 307 molecules ![](data/chem/img/DCA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZNS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZNS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-DCA / | ||||||
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#4: Chemical | ChemComp-EDO / | ||||||
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-ZNS / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 22.5% (w/v) PEG3350, 100 mM ammonium succinate pH 7.5, 100 mM Tris-HCl pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 10, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.58→56.43 Å / Num. obs: 92537 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.16 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Net I/σ(I): 9.5 / Num. measured all: 320245 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6XRU Resolution: 1.58→39.13 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.47 / 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: 126 Å2 / Biso mean: 40.8869 Å2 / Biso min: 15.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→39.13 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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