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Yorodumi- PDB-7cbi: Crystal structure of threonyl-tRNA synthetase (ThrRS) from Salmon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cbi | ||||||
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Title | Crystal structure of threonyl-tRNA synthetase (ThrRS) 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: 1.59 Å | ||||||
Authors | Guo, J. / Chen, B. / Zhou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors. Authors: Guo, J. / Chen, B. / Yu, Y. / Cheng, B. / Ju, Y. / Tang, J. / Cai, Z. / Gu, Q. / Xu, J. / Zhou, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cbi.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cbi.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 7cbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cbi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7cbi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7cbi_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 7cbi_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/7cbi ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cbi | HTTPS FTP |
-Related structure data
Related structure data | 7cbgC 7cbhC 6l2qS 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 , 1 types, 2 molecules AB
#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, A628_05061 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V7II86, threonine-tRNA ligase |
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-Non-polymers , 5 types, 731 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.24 M lithium acetate pH 7.5, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→72.36 Å / Num. obs: 121233 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.59→1.65 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 11978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L2Q Resolution: 1.59→72.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.56 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.294 Å2
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Refinement step | Cycle: 1 / Resolution: 1.59→72.36 Å
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Refine LS restraints |
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