Computational protocol: Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease

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Protocol publication

[…] The crystal was cryoprotected in a solution containing 1.0 M imidazole (pH 7.5), 30% (v/v) glycerol, and flash-frozen at 100 K. X-ray diffraction data were collected at beamline BL26B1 of SPring-8 (Hyogo, Japan) with a Saturn A200 CCD detector, and processed and scaled with HKL2000 (Otwinowski & Minor, 1997).The structure was determined by the TLS-restrained crystallographic refinement with REFMAC5 (Winn et al., 2001) in the CCP4 suite (Winn et al., 2011) using the structure of 1510-N K138A in complex with the 234P10 peptide (PDB code, 3viv) as the initial model by slight model fitting with COOT (Emsley & Cowtan, 2004). The least-squares fitting between two structures was performed with LSQKAB in the CCP4 suite. All molecular figures were produced with PyMOL (http://www.pymol.org/). The atomic coordinates and structure factors have been deposited in the RCSB Protein Data Bank with the accession code 3wg5. […]

Pipeline specifications

Software tools REFMAC5, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Pyrococcus horikoshii, Homo sapiens
Diseases Anemia, Hemolytic, Genetic Diseases, Inborn