Computational protocol: Schistosoma mansoni venom allergen-like protein 4 (SmVAL4) is a novel lipid-binding SCP/TAPS protein that lacks the prototypical CAP motifs

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Protocol publication

[…] X-ray diffraction data were collected at the Baylor College of Medicine core facility using a Rigaku HTC detector. The X-ray source was a Rigaku FR-E+ SuperBright microfocus rotating-anode generator with VariMax HF optics. A data set was collected from a single crystal with a crystal-to-detector distance of 105 mm and exposure times of 120 s for 0.5° oscillations using the CrystalClear (d*TREK) package (Pflugrath, 1999). Data were processed using MOSFLM (Leslie, 2006). The crystal belonged to the tetragonal space group P61, with approximate unit-cell parameters a = 78.65, b = 78.65, c = 83.52 Å, α = β = 90, γ = 120°.As was the case with the other SCP/TAP protein structure solved in our laboratory, several attempts at molecular replacement (MR) were performed using different search models (Asojo et al., 2011, 2005; Asojo, 2011) with Phaser (McCoy et al., 2005; Storoni et al., 2004). The only MR search model that resulted in a solution with an R free of less than 40% was sGLIPR1 (PDB entry 3q2r; Asojo et al., 2011) with major loops removed. The correct MR solution implied a monomer of SmVAL4 per asymmetric unit with a Matthews coefficient (Kantardjieff & Rupp, 2003; Matthews, 1968) of 3.97 Å3 Da−1 and a solvent content of 69%. The model was improved through automatic model building with ARP/wARP (Morris et al., 2003, 2004) followed by manual model-building cycles using Coot (Emsley et al., 2010) and structure refinement with REFMAC5 (Murshudov et al., 2011) within the CCP4 package (Winn et al., 2011). Unless otherwise noted, figures were generated using PyMOL (DeLano, 2002). Details of the quality of the structure as well as data collection are shown in Table 1. The atomic coordinates and structure factors have been deposited in the PDB as entry 4p27. […]

Pipeline specifications

Software tools SHELX, iMosflm, ARP/wARP, Coot, REFMAC5, CCP4, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Schistosoma mansoni, Homo sapiens, Saccharomyces cerevisiae
Diseases Parasitic Diseases, Schistosomiasis, Schistosomiasis mansoni
Chemicals Amino Acids, Cholesterol