Computational protocol: A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA

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Protocol publication

[…] X-ray datasets of the four crystals were collected at 100K with synchrotron radiation at the structural biology beamlines, NW12A, BL-17A and BL-5A, of the Photon Factory (Tsukuba, Japan). Each dataset was processed with the program CrystalClear (Rigaku Americas Corp., TX, USA). The obtained intensity data were further converted to structure-factor amplitudes using the program TRUNCATE from the CCP4 suite (). The statistics of data collections and the crystal data are summarized in Table .The initial phases of the four crystals were derived with the molecular replacement method by using the program AutoMR from the Phenix suite (,). The molecular structures were constructed and manipulated with the programs Coot (,). The atomic parameters of each structure were refined using the program phenix.refine from the Phenix suite (,) through a combination of simulated-annealing, crystallographic conjugate gradient minimization refinements and B-factor refinements. The statistics of structure refinements are summarized in Table . Molecular drawings were made using the program PyMOL (). The atomic coordinates and experimental data of the A1408m1A, A1408m1A-G418, A1408m1A-Paromomycin and A1408m1A-Gentamicin crystals have been deposited in the Protein Data Bank (PDB) with the ID codes 4WCP, 4WCQ, 4WCR and 4WCS, respectively (). […]

Pipeline specifications

Software tools CCP4, PHENIX, Coot, PyMOL
Application Protein structure analysis
Organisms Escherichia coli
Chemicals Aminoglycosides, Gentamicins