Computational protocol: Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly amongst IspD/IspE/IspF enzymes in the MEP pathway

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[…] The structures of BsIspF were elucidated by molecular replacement using PHASER [] from the CCP4 program suite []. The starting model was the monomer IspF enzyme from Shewanella oneidensis (PDB: 1T0A), which shared 62% sequence identity with the BsIspF and served as a good model for the structure solution. Only one solution was evident. Refinement was performed using the maximum likelihood functions implemented in REFMAC5 [], while model building and improvement were achieved with COOT []. Solvent molecules, metal ions and ligands were positioned after a few cycles of refinement. Non-crystallographic symmetry (NCS) restraints were imposed in the early stages of the analyses and then released as the refinements progressed. Isotropic refinement of the atomic displacement parameters was performed for all atoms. The stereochemistry was checked with the program MolProbity []. Details of the overall refinement and final quality of the models are shown in . The program PyMOL (http://www.pymol.sourceforge.net/) was used to prepare structural figures. [...] The cavity analysis was performed using CASTp server [], surface calculations were performed by ArealMol from CCP4 programs suite []. […]

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