Computational protocol: Structure basis 1/2SLPI and porcine pancreas trypsin interaction

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Protocol publication

[…] The purified 1/2SLPI and PPT were mixed with a 1:1 molar ratio in 50 mM Tris-HCl (pH 7.5) and incubated for 2 h at room temperature. The following sample was dialyzed against 50 mM Tris-HCl (pH 7.5) and concentrated to 30 mg ml−1 as PPT and 1/2SLPI complex. The initial crystallization screening was performed by the sitting-drop vapour-diffusion method at 293 K, using Jena Bioscience Screening kits. The appropriate crystals were obtained from 25% PEG4000, 100 mM Na-citrate (pH 5.6), 200 mM ammonium sulfate. X-ray diffraction data were collected by FR-E (Rigaku) from a single frozen crystal. The collected data were processed with CrystalClear version 1.3.5 and solved by the molecular replacement method using the CCP4 version 4.2 suite with the X-ray structure of 1/2SLPI [Protein Data Bank (PDB) code: 2z7f; Koizumi et al., 2008] and the structure of PPT (PDB code: 1avw; Song & Suh, 1998) as search models. Structure refinements were performed with REFMAC5. The quality of the final structures was accessed with PROCHECK prior to depositing at the PDB under the code 4doq. The detailed data-collection statistics are presented in Table 1. […]

Pipeline specifications

Software tools CCP4, REFMAC5, PROCHECK
Applications Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma, Bos taurus
Diseases Infection, HIV Infections