Computational protocol: Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate

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Protocol publication

[…] SmPNP was expressed, purified and crystallized as previously described (Pereira et al., 2003 2005). The soaking solution consisted of 5 mM R1P, 20% PEG 1500, 15 mM sodium acetate buffer pH 4.9 or 5.0 (at the pH of crystal growth) and 20% glycerol. The crystals were maintained in this solution for up to 48 h.X-ray diffraction data were collected at 100 K on beamline MX1 of the LNLS (Campinas, Brazil) using an X-ray wavelength of 1.43 Å. The crystals of the complex SmPNP–R1P diffract up to 2.0 Å resolution. The data were indexed and integrated using the program MOSFLM (Leslie, 1999) and scaled using the program SCALA from the CCP4 suite (Collaborative Computational Project, Number 4, 1994). [...] The SmPNP–R1P complex was solved by molecular replacement employing MOLREP (Vagin & Teplyakov, 2000) and using native SmPNP (1td1) as a search model (Pereira et al., 2005). The refinement was carried out using Phenix (Adams et al., 2002) together with Coot (Emsley & Cowtan, 2004) for model building into σa-weighted 2F o − F c and F o − F c electron density maps. The compounds were automatically placed using the ‘Find Ligand’ routine of Coot; the water molecules were identified and positioned using both Coot and Phenix.Both R and R free were monitored in order to evaluate the validity of the refinement protocol and the stereochemical quality of the model was calculated using Procheck (Laskowski et al., 1993). The coordinates and structure factors have been deposited in the PDB under the code 3fb1. […]

Pipeline specifications

Software tools iMosflm, CCP4, Molrep, PHENIX, Coot, PROCHECK
Applications Small-angle scattering, Protein structure analysis
Organisms Schistosoma mansoni, Homo sapiens
Diseases Hematologic Diseases, Schistosomiasis
Chemicals Guanine, Guanosine, Hydrogen, Inosine, Ribose, Hypoxanthine