Computational protocol: Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA–tRNA interaction

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Protocol publication

[…] The E5-CRD/ImmE5 complex structure was solved by the multiple isomorphous replacement (MIR) method, and it was refined at a 1.9 Å resolution to an R-factor of 17.9% (Rfree = 19.8%). MIR phasing and refinement of the heavy atom positions were carried out using the program MLPHARE, and density modification was performed using the program DM. Iterative rounds of refinement and rebuilding of the native model were performed by using the programs CNS () and QUANTA (Accelrys Inc., San Diego, CA), respectively. The structure of E5-CRD complexed with dGpdUp was determined by the molecular replacement method using the program AMoRe. The E5-CRD coordinates obtained by MIR were used as a target. The programs MLPHARE, DM and AMoRe are included in the CCP4 suite (). The structure was refined at a 1.9 Å resolution to an R-factor of 19.7% (Rfree = 21.7%). Figures 1, 3, 5, 6 and 7 were created using PyMOL (), and Figure 2 was created using Molscript (). The atomic coordinates and structure factors of the E5-CRD/ImmE5 and E5-CRD/dGpdUp complexes have been deposited in the PDB under the accession codes 2DFX and 2DJH, respectively. […]

Pipeline specifications

Software tools CNS, CCP4, PyMOL, MolScript
Applications Drug design, Protein structure analysis
Organisms Escherichia coli
Chemicals Guanine, Hydrogen, Nucleoside Q, Uracil