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Yorodumi- PDB-1cqi: Crystal Structure of the Complex of ADP and MG2+ with Dephosphory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cqi | ||||||
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Title | Crystal Structure of the Complex of ADP and MG2+ with Dephosphorylated E. Coli Succinyl-CoA Synthetase | ||||||
Components | (PROTEIN (SUCCINYL-COA SYNTHETASE ...) x 2 | ||||||
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: 3.3 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 | 1cqi.cif.gz | 231.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cqi.ent.gz | 196.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cqi_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1cqi_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1cqi_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 1cqi_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cqi ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cqi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-PROTEIN (SUCCINYL-COA SYNTHETASE ... , 2 types, 4 molecules ADBE
#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) |
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-Non-polymers , 4 types, 8 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | |
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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: 3.59 Å3/Da / Density % sol: 65.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.3 Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, COENZYME A, pH 7.30, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||
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: Jun 8, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. all: 31753 / Num. obs: 31753 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.164 |
Reflection shell | Resolution: 3.3→3.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.378 / % possible all: 98.4 |
Reflection | *PLUS Num. measured all: 195264 |
Reflection shell | *PLUS Lowest resolution: 3.54 Å / Num. unique obs: 15389 |
-Processing
Software |
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Refinement | Resolution: 3.3→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD REFINEMENT IN CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.217 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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