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Yorodumi- PDB-2fpp: Crystal structure of pig GTP-specific succinyl-CoA synthetase fro... -
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-Basic information
Entry | Database: PDB / ID: 2fpp | ||||||
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Title | Crystal structure of pig GTP-specific succinyl-CoA synthetase from polyethylene glycol with chloride ions | ||||||
Components |
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Keywords | LIGASE / Active site Phosphohistidine residue | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Fraser, M.E. / Hayakawa, K. / Hume, M.S. / Ryan, D.G. / Brownie, E.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Interactions of GTP with the ATP-grasp Domain of GTP-specific Succinyl-CoA Synthetase Authors: Fraser, M.E. / Hayakawa, K. / Hume, M.S. / Ryan, D.G. / Brownie, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fpp.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fpp.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 2fpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fpp ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fpp | 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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-Components
#1: Protein | Mass: 32168.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O19069-2, UniProt: O19069*PLUS, succinate-CoA ligase (GDP-forming) | ||||
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#2: Protein | Mass: 42635.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG2 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P53590, succinate-CoA ligase (GDP-forming) | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% v/v isopropanol, 100 mM ammonium sulfate, 20% w/v polyethylene glycol 400, 100 mM HEPES (pH 7.5 with HCl), VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 12, 2001 / Details: Osmic multilayer mirrors |
Radiation | Monochromator: Osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→100 Å / Num. all: 30772 / Num. obs: 27045 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.114 / Χ2: 1.119 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.35→2.43 Å / % possible obs: 77.3 % / Rmerge(I) obs: 0.374 / Num. unique obs: 2359 / Χ2: 0.851 / % possible all: 0.773 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→100 Å / FOM work R set: 0.821 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 34.793 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.299 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→100 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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Xplor file |
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