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Open data
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Basic information
Entry | Database: PDB / ID: 1jkj | ||||||
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Title | E. coli SCS | ||||||
![]() | (succinyl-CoA synthetase ...) x 2 | ||||||
![]() | LIGASE / CITRIC ACID CYCLE / HETEROTETRAMER / ATP-grasp fold / Rossmann Fold | ||||||
Function / homology | ![]() 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 / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...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 / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fraser, M.E. | ||||||
![]() | ![]() Title: Two glutamate residues, Glu 208 alpha and Glu 197 beta, are crucial for phosphorylation and dephosphorylation of the active-site histidine residue in succinyl-CoA synthetase. Authors: Fraser, M.E. / Joyce, M.A. / Ryan, D.G. / Wolodko, W.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.1 KB | Display | ![]() |
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PDB format | ![]() | 218.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 58.2 KB | Display | |
Data in CIF | ![]() | 81.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jllC ![]() 2scuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Succinyl-CoA synthetase ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 29679.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming) #2: Protein | Mass: 41438.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A836, succinate-CoA ligase (ADP-forming) |
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-Non-polymers , 5 types, 604 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-COA / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.23 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: microdialysis / pH: 7.4 Details: potassium phosphate, ammonium sulfate, pH 7.4, MICRODIALYSIS, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.3 / Details: Wolodko, W.T., (1984) J. Biol. Chem., 259, 5316. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 1999 |
Radiation | Monochromator: cylindrically-bent silicon crystal, cylindrically bent rhodium-coated silicon mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 68244 / Num. obs: 68244 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.5 / % possible all: 73.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 156588 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 73.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2SCU Resolution: 2.35→19.64 Å Cross valid method: Throughout. Started with 10% of the data, reduced this to just over 1000 reflections near the end of the refinement. σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 25.4336 Å2 / ksol: 0.35056 e/Å3 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.46 Å / Rfactor Rfree error: 0.027
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 67088 / σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.269 / % reflection Rfree: 1 % / Rfactor Rwork: 0.269 |