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Yorodumi- PDB-7jkr: GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jkr | ||||||
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Title | GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, phosphohistidine loop pointing towards nucleotide binding site | ||||||
Components |
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Keywords | LIGASE / Complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Huang, J. / Fraser, M.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2021 Title: Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase Authors: Huang, J. / Fraser, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jkr.cif.gz | 395.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jkr.ent.gz | 327.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/7jkr ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jkr | HTTPS FTP |
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-Related structure data
Related structure data | 6xruC 7jfpC 7jj0C 7jmkC 2fp4S 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32089.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O19069, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming) |
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#2: Protein | Mass: 42711.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P53590, succinate-CoA ligase (GDP-forming) |
-Non-polymers , 4 types, 10 molecules
#3: Chemical | ChemComp-GOL / |
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#4: Chemical | ChemComp-GNP / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 1.0 M sodium citrate, Tris-HCl pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→86.02 Å / Num. obs: 23016 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.64→2.69 Å / Rmerge(I) obs: 2.191 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1140 / CC1/2: 0.298 / Rpim(I) all: 0.938 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FP4 Resolution: 2.64→86.02 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 244.11 Å2 / Biso mean: 117.901 Å2 / Biso min: 52.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.64→86.02 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: -7.493 Å / Origin y: 27.9591 Å / Origin z: 12.7257 Å
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Refinement TLS group |
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