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Yorodumi- PDB-1jll: Crystal Structure Analysis of the E197betaA Mutant of E. coli SCS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jll | ||||||
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Title | Crystal Structure Analysis of the E197betaA Mutant of E. coli SCS | ||||||
Components | (succinyl-CoA synthetase ...Succinyl coenzyme A synthetase) x 2 | ||||||
Keywords | LIGASE / CITRIC ACID CYCLE / HETEROTETRAMER / ATP-GRASP FOLD / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.69 Å | ||||||
Authors | Fraser, M.E. | ||||||
Citation | Journal: Biochemistry / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jll.cif.gz | 262.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jll.ent.gz | 210.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jll ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jll | HTTPS FTP |
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-Related structure data
Related structure data | 1jkjSC 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 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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming) #2: Protein | Mass: 41380.461 Da / Num. of mol.: 2 / Mutation: E197A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P0A836, succinate-CoA ligase (ADP-forming) |
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-Non-polymers , 4 types, 203 molecules
#3: Chemical | #4: Chemical | ChemComp-COA / #5: Chemical | ChemComp-SO4 / #6: 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: 3.23 Å3/Da / Density % sol: 61.88 % | ||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2000 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 48720 / Num. obs: 48720 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.6 / % possible all: 61.7 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 152728 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / % possible obs: 61.7 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1JKJ, partially refined Resolution: 2.69→34.38 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: 43.6307 Å2 / ksol: 0.380601 e/Å3 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.69→34.38 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.339 / Rfactor Rwork: 0.34 / Total num. of bins used: 4
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 47023 / 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: 0.339 / Rfactor Rwork: 0.34 |