+Open data
-Basic information
Entry | Database: PDB / ID: 2nu8 | ||||||
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Title | C123aT Mutant of E. coli Succinyl-CoA Synthetase | ||||||
Components | (Succinyl-CoA ...) x 2 | ||||||
Keywords | LIGASE / citric acid cycle / heterotetramer / ATP-GRASP fold / Rossmann fold | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Fraser, M.E. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007 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 1325 were not modeled due to lack of electron density. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nu8.cif.gz | 270.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nu8.ent.gz | 216.4 KB | Display | PDB format |
PDBx/mmJSON format | 2nu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nu8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2nu8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2nu8_validation.xml.gz | 56.5 KB | Display | |
Data in CIF | 2nu8_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nu8 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nu8 | HTTPS FTP |
-Related structure data
Related structure data | 2nu6C 2nu7C 2nu9C 2nuaC 1jkjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 29677.201 Da / Num. of mol.: 2 / Mutation: C123T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sucD / Plasmid: pGS202 / Production host: Escherichia coli (E. coli) / Strain (production host): TK3D18 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.) Escherichia coli (E. coli) / Gene: sucC / Plasmid: pGS202 / Production host: Escherichia coli (E. coli) / Strain (production host): TK3D18 References: UniProt: P0A836, succinate-CoA ligase (ADP-forming) |
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-Non-polymers , 5 types, 521 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-COA / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.19 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: BICINE, Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9474 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 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: 2.15→100 Å / Num. all: 94811 / Num. obs: 94811 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 31.97 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2681 / % possible all: 51.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1JKJ Resolution: 2.15→41.97 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→41.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Rfactor Rfree error: 0.011
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