July 2023 issue
It is shown that checkMySequence, an automated method for validating sequence assignment in cryo-EM structures of proteins, can be used to validate crystal structure models.
An integrative framework called Flexibility Hub is integrated into Scipion that simplifies the interoperability of different heterogeneity algorithms.
Structures of mannose 2-epimerase and a mutant from Runella slithyformis were determined in their apo form and in complex with D-glucitol. In combination with a biochemical assay, the molecular basis of the substrate specificity and activity of the enzyme was elucidated.
The single-component flavin-dependent tryptophan halogenase AetF converts tryptophan to 5,7-dibromotryptophan during the biosynthesis of the neurotoxin aetokthonotoxin. Crystal structures of AetF with the substrates tryptophan and 5-bromotryptophan show that a flip of the indole moiety of tryptophan positions first C5 and then C7 in the same location in the active site to facilitate two successive bromination reactions.
In this work, a novel method to recover the diffraction phase independently using the low-resolution data is proposed. It has been verified and found to be useful and practical using several typical examples. In addition, a practical metric has been established to determine whether the algorithm converges to a correct solution by estimating the entropy of the final results.
Calixarene-mediated protein assembly provides a basis for the development of new types of biomaterials. A fourth structure of the Ralstonia solanacearum lectin–sulfonato-calixarene complex expands the crystal-engineering landscape and suggests an alternative pH trigger of assembly.
The crystal structure of the monocupin 5-nitrosalicylate 1,2-dioxygenase, an iron(II)-dependent ring-cleaving dioxygenase, from Bradyrhizobium sp. was determined by molecular replacement using a theoretical model obtained by AlphaFold2. Comparison with structures of other members of the same class and docking of the substrate allowed identification of the residues responsible for its very unusual enzyme selectivity.
The crystal structure of a novel laccase-like multicopper oxidase from the thermophilic fungus Thermothelomyces thermophila was refined at 1.9 Å resolution. Ligand-docking simulations reveal conformational changes that influence substrate specificity.
The refinement and validation of nine A-form DNA 18-mer crystal structures containing both canonical and noncanonical base pairs benefits from the use of dinucleotide conformer classes (NtCs).
addenda and errata
The article by Afonine et al. [Acta Cryst. (2013). D69, 625–634] is corrected.