Computational protocol: Structural Basis for the Activity and Substrate Specificity of Fluoroacetyl-CoA Thioesterase FlK

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Protocol publication

[…] Data for apo-form WtFlK and SeMet FlK were collected at beamline ID14.4, European Synchrotron Radiation Facility (Grenoble, France). The data sets were processed using DENZO and SCALEPACK (version 1.97) (). The data were truncated and converted to structure factors using TRUNCATE () from the CCP4 suite (). X-ray data for complexes of WtFlK·FAc, T42AFlK·FAc, T42SFlK·AcCoA, WtFlK·FAcCPan, and WtFlK·FAcOPan were collected at the Swiss Light Source, and the WtFlK·Ac, T42SFlK·Ac, and T42SFlK·FAc were collected at the European Synchrotron Radiation Facility. The data sets were processed using the program Mosflm () and scaled by SCALA (). The structure of SeMet FlK in its apo-form was solved using single-wavelength anomalous diffraction and the Phenix program (), and the other structures were solved by molecular replacement using the apo-structure as probe search in the program AMoRe () in the CCP4 suite (). The refinement was carried out using the program REFMAC 5.2 (). Visual inspection and water addition were performed using XtalView/xfit () and Coot (). The quality of the model was assessed using PROCHECK (). The figures were made using PyMOL (). […]

Pipeline specifications

Software tools CCP4, iMosflm, PHENIX, Coot, PROCHECK, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Streptomyces cattleya, Canis lupus familiaris
Chemicals Acetyl Coenzyme A, Fluorine