Computational protocol: Structure of nitrilotriacetate monooxygenase component B from Mycobacterium thermoresistibile

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Protocol publication

[…] A crystal was harvested, cryoprotected using precipitant solution supplemented with 20% glycerol and vitrified in liquid nitrogen. A 1.6 Å resolution data set was collected under a stream of liquid nitrogen on Advanced Light Source (ALS) beamline 5.0.2 as part of the ALS Collaborative Crystallography program (Table 1). The data were reduced with HKL-2000 (Otwinowski & Minor, 1997). The structure (Table 2) was solved by molecular replacement using Bacillus thermoglucosidasius A7 flavin reductase A2 protein-only dimer from molecules A and B of PDB entry 1rz0 (van den Heuvel et al., 2004) as a search model in Phaser (McCoy et al., 2007) from the CCP4 suite (Winn et al., 2011). The asymmetric unit was comprised of two independent dimers. The final model was obtained after numerous iterative rounds of refinement in REFMAC (Murshudov et al., 2011) and manual rebuilding in Coot (Emsley & Cowtan, 2004). The final model contained residues Ala3–Ala181 with no internal gaps for protomer A and a few additional protein residues for each of the other three protomers. In addition, the final model contained one glycerol molecule (bound to protomer D) and 548 water molecules. The structure was assessed and corrected for geometry and fitness using MolProbity (Chen et al., 2010). Data-collection results and structure-refinement statistics are listed in Tables 1 and 2. […]

Pipeline specifications

Software tools HKL-2000, CCP4, Coot, MolProbity
Application Protein structure analysis
Organisms Mycobacterium tuberculosis, Homo sapiens
Diseases Tuberculosis
Chemicals Carbon, Flavins, Flavin Mononucleotide, NAD, Nitrogen