Computational protocol: Further Characterization of Functional Domains of PerA, Role of Amino and Carboxy Terminal Domains in DNA Binding

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Protocol publication

[…] A computational model of the three-dimensional structure of PerA (P43459) was built with the CPHmodels 3.0 Server (http://www.cbs.dtu.dk/services/CPHmodels) . After an initial search, CPHmodels defined the E. coli transcriptional factor Rob (PDB entry 1D5Y chain A) as the best hit to be used as a template. These two proteins share 27% of identity (data not shown). In order to refine the model, this was minimized by using the Gromacs server (http://lorentz.immstr.pasteur.fr/gromacs) . Finally, the RAMPAGE program (http://mordred.bioc.cam.ac.uk/~rapper) was used to validate the stereochemical quality of the resulting three-dimensional model . After analyzing the Ramachandran plot, 98.2% of the residues were located in allowed regions. All the bond distances, angles and dihedrals fulfill the normal limits for polypeptide chains. The resulting model includes 112 of the 274 residues at the carboxyl terminus of PerA. Finally, the structure was displayed in ribbon by using Pymol program. […]

Pipeline specifications

Software tools CPHmodels, GROMACS, PyMOL
Application Protein structure analysis
Organisms Escherichia coli