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Yorodumi- PDB-1cqj: CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cqj | ||||||
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Title | CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE | ||||||
Components |
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Keywords | LIGASE / 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 / Resolution: 2.9 Å | ||||||
Authors | Joyce, M.A. / Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography. Authors: Joyce, M.A. / Fraser, M.E. / James, M.N. / Bridger, W.A. / Wolodko, W.T. #1: Journal: J.Mol.Biol. / Year: 1999 Title: A Detailed Structural Description of Escherichia Coli Succinyl-CoA Synthetase Authors: Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T. #2: Journal: J.Biol.Chem. / Year: 1994 Title: The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5A resolution Authors: Wolodko, W.T. / Fraser, M.E. / James, M.N.G. / Bridger, W.A. #3: Journal: J.Biol.Chem. / Year: 1984 Title: Crystallization of succinyl-CoA synthetase from Escherichia coli Authors: Wolodko, W.T. / James, M.N.G. / Bridger, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cqj.cif.gz | 258 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cqj.ent.gz | 216.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cqj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1cqj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1cqj_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 1cqj_validation.cif.gz | 76.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cqj ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cqj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Heterotetramer formed by two alpha beta-dimers related by a crystallographic two-fold axis. |
-Components
#1: Protein | Mass: 29436.902 Da / Num. of mol.: 2 / Fragment: ALPHA SUBUNIT 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: 41123.152 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P07460, UniProt: P0A836*PLUS, succinate-CoA ligase (ADP-forming) #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.85 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: microdialysis / pH: 7.3 Details: ammonium sulfate, potassium phosphate, coenzyme A, pH 7.3, MICRODIALYSIS, temperature 294K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Dec 4, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 45002 / Num. obs: 45002 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Num. unique all: 6283 / % possible all: 96.6 |
Reflection | *PLUS % possible obs: 98.7 % / Num. measured all: 258739 |
Reflection shell | *PLUS Lowest resolution: 3.08 Å / Num. measured obs: 19746 |
-Processing
Software |
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Refinement | Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood refinement in CNS
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |