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Yorodumi- PDB-8h9c: Crystal structure of chemically modified E. coli ThrS catalytic d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h9c | ||||||
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Title | Crystal structure of chemically modified E. coli ThrS catalytic domain 4 | ||||||
Components | Threonine--tRNA ligase | ||||||
Keywords | LIGASE / Threonine--tRNA ligase | ||||||
Function / homology | Function and homology information threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Qiao, H. / Xia, M. / Wang, J. / Fang, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h9c.cif.gz | 182.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h9c.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 8h9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h9c_validation.pdf.gz | 769 KB | Display | wwPDB validaton report |
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Full document | 8h9c_full_validation.pdf.gz | 774.8 KB | Display | |
Data in XML | 8h9c_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 8h9c_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/8h9c ftp://data.pdbj.org/pub/pdb/validation_reports/h9/8h9c | HTTPS FTP |
-Related structure data
Related structure data | 8h98C 8h99C 8h9aC 8h9bC 1fyfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47921.535 Da / Num. of mol.: 1 / Fragment: UNP residues 242-642 / Mutation: Y462R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: E2QMS9, threonine-tRNA ligase |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ...Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ethylene glycol, 10% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97856 Å |
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: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. obs: 12955 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.14→2.2 Å / Rmerge(I) obs: 0.778 / Num. unique obs: 2446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FYF Resolution: 2.15→48.14 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 24.96 / 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: 37.95 Å2 / Biso mean: 18.7157 Å2 / Biso min: 8.68 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→48.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 41.9046 Å / Origin y: 1.374 Å / Origin z: 8.1045 Å
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Refinement TLS group |
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