Computational protocol: Novel UDP GalNAc Derivative Structures Provide Insight into the Donor Specificity of Human Blood Group Glycosyltransferase*

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Protocol publication

[…] X-ray diffraction data were collected to 1.9-Å resolution on the AAGlyB-3 complex at beamline I911-2 at the MAX II synchrotron in Lund, Sweden (λ = 1.038 Å, 100 K). X-ray diffraction data on the AAGlyB-3-HAA complex was collected to 1.65-Å resolution at beamline BL14.1 at the BESSY II synchrotron in Berlin, Germany (λ = 0.918 Å, 100 K). Both data sets were integrated and scaled by XDS (). Subsequently, the structures were solved by molecular replacement using the module Phaser () including the solved structure of wild-type GTB (PDB entry 2RIT) as a search model. The two structures belong to space group P21212 with two molecules in the asymmetric unit. Restrained refinement was initially carried out in REFMAC5 () before iteratively rebuilding the structures using Coot () and finally refining in Phenix () with TLS included. Ramachandran plots were calculated in PROCHECK () and show that all residues are within the allowed region in both structures. The crystallographic details are presented in . The structural figures were all prepared in PyMOL (DeLano Scientific LLG). […]

Pipeline specifications

Software tools REFMAC5, Coot, PHENIX, PROCHECK, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Homo sapiens
Chemicals Amino Acids, Hydrogen, Uridine Diphosphate, Uridine Diphosphate Galactose