Computational protocol: Crystal structure of the NurA–dAMP–Mn2+ complex

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Protocol publication

[…] Pf NurA structure was determined by single-wavelength anomalous scattering dispersion (SAD) method using Se-Met-derivatized crystals. Fourteen selenium sites were identified in the asymmetric unit, and the apo Pf NurA structure was determined with the PHENIX program (). After flattening the solvent, a high-quality electron density map with a resolution of 2.82 Å was obtained. Successive rounds of model building using COOT () and refinement using CNS () and PHENIX were performed to build the complete model. Restrained NCS was applied throughout the refinement. The final apo- model consists of 860 residues, seven glycerol molecules and 19 water molecules. The structure of Mn2+-bound Pf NurA and dAMP–Mn2+-bound Pf NurA were determined by difference Fourier methods using the apo–Pf NurA structure. The Mn2+-bound Pf NurA consists of 845 residues, four Mn2+ ions, one glycerol molecule and 20 water molecules. The dAMP and Mn2+-bound model consists of 865 residue, two Mn2+ ions, one dAMP molecule, one glycerol molecule and nine water molecules. The N-terminal His-tagged residues were not visible and were presumably disordered. The statistics are summarized in Supplementary Table S1. Missing residues in each structure are described in the Supplementary Data (Information on substrates, nuclease assays, analytical ultracentrifugation and mutant protein structural analysis is described in the Supplementary Data). […]

Pipeline specifications

Software tools PHENIX, Coot, CNS
Application Protein structure analysis
Chemicals Ribose