Computational protocol: Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design

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Protocol publication

[…] Data were collected on beamlines I911-2 and I911-3 at the MAX-lab synchrotron facility in Lund. Processing and scaling were performed with XDS (Kabsch, 2010). Phaser (McCoy et al., 2007) was used for solving the structures by molecular replacement using the coordinates of PDB entry 2i7c (Dufe et al., 2007) as a search model. The structures were refined with REFMAC5 (Murshudov et al., 2011) and rebuilt using Coot (Emsley & Cowtan, 2004). Model validation was performed using the integrated validation tools in PHENIX (Urzhumtseva et al., 2009; Adams et al., 2010; Chen et al., 2010). […]

Pipeline specifications

Software tools XDS, REFMAC5, Coot, PHENIX
Applications Small-angle scattering, Protein structure analysis
Organisms Plasmodium falciparum, Dipturus trachyderma
Diseases Malaria
Chemicals Putrescine, Spermidine