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Open data
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Basic information
Entry | Database: PDB / ID: 2nu7 | ||||||
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Title | C123aS Mutant of E. coli Succinyl-CoA Synthetase | ||||||
![]() | (Succinyl-CoA ...) 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: Participation of Cys 123alpha of Escherichia coli Succinyl-CoA Synthetase in Catalysis Authors: Hidber, E. / Brownie, E.R. / Hayakawa, K. / Fraser, M.E. | ||||||
History |
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Remark 600 | HETEROGEN Atoms missing from COA 1025 and 1325 were not modeled due to lack of electron density. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.9 KB | Display | ![]() |
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PDB format | ![]() | 214.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 76.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nu6C ![]() 2nu8C ![]() 2nu9C ![]() 2nuaC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Succinyl-CoA ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 29663.178 Da / Num. of mol.: 2 / Mutation: C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AGE9, 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 , 4 types, 371 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-COA / #5: Chemical | ChemComp-SO4 / #6: 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: 61.24 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2002 / Details: monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9474 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. all: 88752 / Num. obs: 88752 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3140 / % possible all: 64.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2SCU Resolution: 2.2→23.45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→23.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.01
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