Computational protocol: RRP6 from Trypanosoma brucei: Crystal Structure of the Catalytic Domain, Association with EAP3 and Activity towards Structured and Non-Structured RNA Substrates

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Protocol publication

[…] The structure of TbRRP6CAT was solved by molecular replacement with the program PHASER using the atomic coordinates of the human RRP6 (PDB code 3SAF) as the search model. Rigid body refinement using the model of the native TbRRP6CAT was applied in order to obtain the initial electron density map for the mutant TbRRP6CAT-C496S. Refinement of the structures were performed alternating cycles of BUSTER with visual inspection and manual rebuilding using COOT . For TbRRP6CAT, a total of 359 residues, out of the 365 expected excluding the His-tag fusion, were modeled for one monomer in the asymmetric unit. 185 water molecules were added during the refinement cycles and the Rfactor/Rfree values converged to 0.16/0.22. For the mutant TbRRP6CAT-C496S, 355 residues and 212 water molecules were modeled in the asymmetric unit and the Rfactor/Rfree values converged to 0.17/0.22. The stereochemistry of the models was analyzed with MolProbity and no outliers were observed in the Ramachandran plot. Refinement statistics are summarized in the . Electrostatic potential were calculated using the Adaptive Poisson-Boltzmann Solver through the PDB2PQR Server . […]

Pipeline specifications

Software tools Coot, MolProbity, PDB2PQR
Application Protein structure analysis
Organisms Trypanosoma brucei, Saccharomyces cerevisiae