Computational protocol: An Appended Domain Results in an Unusual Architecture for Malaria Parasite Tryptophanyl-tRNA Synthetase

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Protocol publication

[…] We generated atomic model of Pf-WRS AXD domain using P. horikoshii Ala-X like homolog structure (PDB: 1WNU) and the software MODELLER. Pf-WRS crystals were obtained at 20°C by hanging drop vapor diffusion method using 1 µl of Pf-WRS(8.5 mg/ml) and 1 µl of 0.09 M NPS (0.03 M NaNO3+0.03 M ammonium sulfate+0.0.3 M Na2HPO4), 0.1 M bicin pH 8.5, 12.5% MPD, 12.5%w/v PEG 1000, 12.5%w/v PEG 3350. Plate-shaped single crystals were directly mounted in cooled nitrogen gas at 100K. X-ray diffraction data were collected on a MARCCD detector at BM14 beam line of European Synchrotron Radiation Facility at Grenoble, France. The diffraction images were processed and scaled with HKL2000 suite program . Initial model was build by AutoBuild in PHENIX which was subsequently rebuilt manually using COOT . Model refinement was performed using phenix.refine in PHENIX. All the structural superimposition and preparation of figures was been carried out using UCSF chimera . […]

Pipeline specifications

Software tools MODELLER, PHENIX, Coot, UCSF Chimera
Applications Small-angle scattering, Protein structure analysis
Organisms Plasmodium falciparum, Toxoplasma gondii
Chemicals Amino Acids