Computational protocol: The periplasmic binding protein NrtT affects xantham gum production and pathogenesis in Xanthomonas citri

Similar protocols

Protocol publication

[…] The genome organization of operons from different species and primary sequence of the proteins were obtained from the KEGG database (http://www.genome.jp/kegg/). A search for proteins with sequence similarity was made with the blastp program using non‐redundant search and similar proteins with resolved structure were found using blastp against the Protein Data Bank (PDB) . Amino acid sequence alignment was performed using clustal omega . The three‐dimensional model of NrtT was built using the modeller program based on the structural coordinates of the X. citri alkanesulfonate‐binding protein SsuA2 (PDB code 3E4R). Model validation was performed using tools from the wincoot program . Figures were drawn using the pymol program . [...] NrtT small angle X‐ray scattering (SAXS) analyses in the absence and presence of MOPS were carried out on the SAXS1 beamline of the Brazilian National Laboratory of Synchrotron Light (LNLS; Campinas, SP, Brazil). Measurements of buffers and samples were made at room temperature with exposure time of 300 s. Samples were prepared with 10 μm of NrtT and 30 μm of MOPS. Subtraction of buffers spectra was obtained with the fit‐2d program . Envelopes were determined from ab initio molecular modeling using the atsas 2.1 software package and the graphs were constructed in the program originpro 8 (OriginLab Corp., Northampton, MA, USA). The rigid body model was created from the coral program, included in the atsas 2.1 package, and the generated structure was observed in the pymol program. […]

Pipeline specifications

Software tools BLASTP, Clustal Omega, MODELLER, PyMOL, ATSAS
Databases KEGG
Applications Small-angle scattering, Protein structure analysis
Organisms Xanthomonas citri
Chemicals Adenosine Triphosphate, Sulfur