Computational protocol: A new class of inhibitors of the AraC family virulence regulator Vibrio cholerae ToxT

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Protocol publication

[…] Data sets were collected remotely at beam line GM/CA-XSD 23-ID-B at the Advanced Light Source at Argonne National Laboratory. Diffraction data were indexed and integrated with X-ray Detector Software (XDS) and merged using Phenix. Molecular replacement solutions were obtained with Phenix Phaser-MR using ToxT (PDB ID 3GBG) with PAM deleted from the PDB. The initial model was built via Phenix AutoBuild. Ligands were built from their SMILES strings using Phenix eLBOW. The corresponding CIF files were viewed and edited in Phenix REEL. Ligands were manually placed into the electron density using Coot and visualized using Pymol. Iterative model refinement was performed using Phenix and Coot. Molecules of MES buffer were positioned in a similar manner as the ligands. Data collection and refinement statistics are presented in . […]

Pipeline specifications

Software tools XDS, PHENIX, Coot, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Vibrio cholerae, Homo sapiens, Bacteria
Diseases Dysentery, Infection