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Yorodumi- PDB-7wmi: Threonyl-tRNA synthetase from Salmonella enterica in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wmi | |||||||||
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Title | Threonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor | |||||||||
Components | Threonine--tRNA ligase | |||||||||
Keywords | LIGASE/INHIBITOR / LIGASE-Inhibitor complex | |||||||||
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 | Salmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Cai, Z. / Chen, B. / Yu, Y. / Zhou, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors against Aminoacyl-tRNA Synthetases. Authors: Cai, Z. / Chen, B. / Yu, Y. / Guo, J. / Luo, Z. / Cheng, B. / Xu, J. / Gu, Q. / Zhou, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wmi.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wmi.ent.gz | 143.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wmi_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7wmi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7wmi_validation.xml.gz | 33 KB | Display | |
Data in CIF | 7wmi_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wmi ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wmi | HTTPS FTP |
-Related structure data
Related structure data | 7wm7C 7wmfC 6l2qS 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
#1: Protein | Mass: 47964.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria) Gene: thrS / Production host: Escherichia coli (E. coli) / References: UniProt: V7II86, threonine-tRNA ligase #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.35 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.28 M lithium acetate pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 61714 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.043 / Rrim(I) all: 0.112 / Χ2: 1.216 / Net I/σ(I): 5.6 / Num. measured all: 407311 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L2Q Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.441 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.07 Å2 / Biso mean: 27.618 Å2 / Biso min: 15.71 Å2
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Refinement step | Cycle: final / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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