Computational protocol: Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent

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Protocol publication

[…] The diffraction data sets of the complex AgnB2 LeuRS-tRNALeu-Leu-AMS were collected at the European Synchrotron Radiation Facility (ESRF, France). The data sets were integrated and scaled with the XDS suite. Further data analysis was performed with the CCP4 suite. The structure was initially solved by molecular replacement with PHASER using as a model the catalytic and anticodon-binding domains of a model built with SWISS-Model based on homology to LeuRSTt (PDB 2BTE) and LeuRSEc (PDB: 4AS1). The molecular replacement solution was used to search with PHASER for AgnB2 tRNALeu using as a model the core of E. coli tRNALeu (bases 1–73, except the bases belonging to the long-variable arm). The obtained model was completed by manual placing of the ZN1 domain, leucine-specific domain, C-terminal domain and editing domain. Manual adjustments were done with COOT and the final model was refined using REFMAC5 (ref. ). Structure quality was analysed with MOLPROBITY ( and showed all residues in allowed regions. Figures were drawn with PYMOL ( […]

Pipeline specifications

Software tools XDS, CCP4, SWISS-MODEL, Coot, REFMAC5, MolProbity, PyMOL
Applications Small-angle scattering, Protein structure analysis
Diseases Neoplasms