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Yorodumi- PDB-1euc: CRYSTAL STRUCTURE OF DEPHOSPHORYLATED PIG HEART, GTP-SPECIFIC SUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1euc | ||||||
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Title | CRYSTAL STRUCTURE OF DEPHOSPHORYLATED PIG HEART, GTP-SPECIFIC SUCCINYL-COA SYNTHETASE | ||||||
Components | (SUCCINYL-COA SYNTHETASE, ...Succinyl coenzyme A synthetase) x 2 | ||||||
Keywords | LIGASE / GTP-specific | ||||||
Function / homology | Function and homology information succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / GTP binding / mitochondrion / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Phosphorylated and dephosphorylated structures of pig heart, GTP-specific succinyl-CoA synthetase. Authors: Fraser, M.E. / James, M.N. / Bridger, W.A. / 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 | 1euc.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1euc.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 1euc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/1euc ftp://data.pdbj.org/pub/pdb/validation_reports/eu/1euc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is an alpha, beta-dimer constructed of chains A and B. |
-Components
-SUCCINYL-COA SYNTHETASE, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 32803.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: HEART / Plasmid: PET-3B / Production host: Escherichia coli (E. coli) References: UniProt: O19069, succinate-CoA ligase (GDP-forming) |
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#2: Protein | Mass: 42810.996 Da / Num. of mol.: 1 / Mutation: L23V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: HEART / Plasmid: PET-3B / Production host: Escherichia coli (E. coli) References: UniProt: P53590, succinate-CoA ligase (GDP-forming) |
-Non-polymers , 4 types, 208 molecules
#3: Chemical | ChemComp-PO4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.84 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis Details: sodium,potassium(1:3) phosphate, 2-mercaptoethanol, ammonium sulfate, MICRODIALYSIS, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / PH range low: 7.4 / PH range high: 7.3 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: 279-283 |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 1, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→59 Å / Num. all: 37771 / Num. obs: 37771 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.109 |
Reflection shell | Resolution: 2.09→2.13 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.307 / Num. unique all: 2027 / % possible all: 71 |
Reflection | *PLUS Num. all: 52273 / Num. measured all: 213996 |
Reflection shell | *PLUS % possible obs: 71 % |
-Processing
Software |
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Refinement | Resolution: 2.1→59 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→59 Å
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Refine LS restraints |
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