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- PDB-7jkr: GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, ph... -
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Open data
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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 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, J. / Fraser, M.E. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 395.7 KB | Display | ![]() |
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PDB format | ![]() | 327.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: O19069, ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P53590, ![]() |
-Non-polymers , 4 types, 10 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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