Computational protocol: Asymmetric Structure of the Dimerization Domain ofPhoR, a Sensor Kinase Important for the Virulence of Mycobacterium tuberculosis

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Protocol publication

[…] X-ray data were collected at National Synchrotron Light Source, Brookhaven National Laboratory. A set of data were collected on a native crystal at beamline X6A, and another set of single wavelength anomalous data were collected at beamline X25 on a SeMet-labeled crystal (). All crystals were in the same space group with identical cell parameters. There were two polypeptide chains per asymmetric unit, with a Matthews volume of ∼2.28 Å3/Da and a solvent content of 46%. The data were processed using HKL2000.The structure was determined using the single-wavelength anomalous diffraction phasing method with the SeMet data set. There are four methionine residues per PhoRD chain. Data output from HKL2000 was imported into the CCP4 format, and phases and initial maps were calculated with SHELXC/D/E. Automatic model building by ArpWarp built 140 out of a total of 148 residues in two polypeptide chains with an R factor of 0.287. The model was manually adjusted using COOT and refined using REFMAC. The native data set was phased by molecular replacement with Phaser and using the structure determined from the SeMet data set as the search model. The structural refinement statistics are listed in . […]

Pipeline specifications

Software tools CCP4, SHELX, Coot
Application Protein structure analysis
Diseases Tuberculosis