Computational protocol: Structural basis for self-assembly of a cytolytic pore lined by protein and lipid

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[…] Data collection was carried out at beamlines BL-5A, AR-NE3A and AR-NW12 of the Photon Factory (Tsukuba, Japan) under cryogenic conditions (100 K). The structure of the water-soluble form was determined by the molecular replacement method using the coordinates of FraC (PDB entry code 3LIM) with PHASER. For the other crystal structures, the coordinates of the water-soluble monomer were used as the initial model for the molecular replacement step. The coordinates were refined with REFMAC5 (ref. ) and COOT from the CCP4 suite. The quality of the final model was assessed with COOT and PROCHECK, as well as with the validation tools provided by the Protein Data Bank. The coordinates and topology file of DHPC and SM were generated with PRODRG. Data collection and refinement statistics are shown in . We note that the structure of the transmembrane pore was modelled with 17 water molecules (2.4% of the total number of residues in the asymmetric unit). Of the 17 water molecules modelled, 15 are conserved in the higher resolution structures of the water-soluble monomer or the lipid-bound form. The additional two water molecules engage the crucial L1 lipid, and together with the L1 lipid itself, are not observed in the high-resolution structures. […]

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