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- PDB-8h9a: Crystal structure of chemically modified E. coli ThrS catalytic d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h9a | ||||||
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Title | Crystal structure of chemically modified E. coli ThrS catalytic domain 2 | ||||||
![]() | Threonine--tRNA ligase | ||||||
![]() | LIGASE / Threonine--tRNA ligase | ||||||
Function / homology | ![]() threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qiao, H. / Xia, M. / Wang, J. / Fang, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tyrosine-targeted covalent inhibition of a tRNA synthetase aided by zinc ion. Authors: Qiao, H. / Xia, M. / Cheng, Y. / Zhou, J. / Zheng, L. / Li, W. / Wang, J. / Fang, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.1 KB | Display | ![]() |
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PDB format | ![]() | 144.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 731 KB | Display | ![]() |
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Full document | ![]() | 734.6 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h98C ![]() 8h99C ![]() 8h9bC ![]() 8h9cC ![]() 1fyfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47893.523 Da / Num. of mol.: 1 / Fragment: UNP residues 242-642 / Mutation: Y462K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-X5V / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2.0 M smmonium sulfate, 0.15 M sodium citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 25514 / % possible obs: 98.1 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.89→1.94 Å / Rmerge(I) obs: 0.606 / Num. unique obs: 2980 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FYF Resolution: 1.9→42.87 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.36 Å2 / Biso mean: 28.9811 Å2 / Biso min: 7.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→42.87 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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