Computational protocol: The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity

Similar protocols

Protocol publication

[…] X-ray diffraction data were collected on an ADSC charge-coupled device at the X29A beamline of National Synchrotron Light Source (NSLS). The diffraction images were processed and scaled with the HKL package . The atomic coordinates of the KlRtr1 structure have been deposited in the Protein Data Bank under the accession code 4FC8.Multiple-wavelength anomalous diffraction (MAD) data sets were collected on the KlRtr1 crystal to 2.5 Å resolution, at the zinc absorption edge (inflection point, 1.2836 Å), peak (1.2833 Å) and remote (1.2652 Å) wavelengths. The data processing statistics are summarized in . The Zn sites were located with the program BnP . Reflection phases were calculated using the program SOLVE/RESOLVE . The complete atomic model was fit into the electron density with the programs O and Coot . The structure refinement was carried out with the programs CNS and Refmac , against the data set at the peak wavelength. The statistics on the structure refinement are summarized in . For the final atomic model, 95.2% of the residues are in the most favored region of the Ramachandran plot, 4.8% in additional allowed regions, and none in the disallowed region.For the AgRtr1 crystal, a single-wavelength anomalous diffraction (SAD) data set to 3.5 Å resolution was collected at the zinc peak wavelength. An electron density map was obtained based on the SAD data, which showed clear indications for several helices. The atomic model of KlRtr1 could be readily positioned into the density, revealing an extra helix in the C-terminal region in the AgRtr1 structure. Refinement of this structure model was not carried out due to the limited resolution. […]

Pipeline specifications

Software tools Coot, CNS
Applications Small-angle scattering, Protein structure analysis
Organisms Saccharomyces cerevisiae, Homo sapiens, Kluyveromyces lactis