Computational protocol: Interaction of Rio1 Kinase with Toyocamycin Reveals a Conformational Switch That Controls Oligomeric State and Catalytic Activity

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Protocol publication

[…] AfRio1-toyocamycin crystals were flash frozen in well solution containing 20% (v/v) glycerol. Data was collected at 100 K at the NE-CAT beamline at the Advanced Photon Source (APS), Argonne, IL, USA. All data was indexed, integrated and scaled using HKL2000 program . Data statistics are provided in . A previously solved structure of afRio1 bound to ATP and Mn2+ (PDB ID: 1ZP9) was used as a molecular replacement model to phase the afRio1-toyocamycin complex structure. The afRio1-toyocamycin data set was phased using MOLREP – as part of CCP4i and subjected to several rounds of building using the model-building program COOT and several rounds of refinement using REFMAC5 and PHENIX , . Data collection and refinement statistics are provided in . The coordinates and structure factors have been deposited in the Protein Data Bank (PDB ID: 3RE4). […]

Pipeline specifications

Software tools Molrep, Coot, REFMAC5, PHENIX
Application Protein structure analysis
Organisms Archaeoglobus fulgidus, Homo sapiens, Dipturus trachyderma
Chemicals Adenosine, Adenosine Triphosphate, Toyocamycin