February 2023 issue
The template tables for small-angle scattering data have been updated by Trewhella et al. [(2023), Acta Cryst. D79 122–132].
In situ quantum-mechanical optimization of ligand structures provides accurate ligand restraints for macromolecular refinement.
SARS-CoV-2 spike protein comprises a conserved hydrophobic pocket that binds linoleic acid (LA). LA supplementation interferes with viral entry into the cell and replication, and thus could be used as an antiviral.
An updated template reporting table based on the 2017 publication guidelines for biomolecular SAS and 3D modelling is presented that includes standard descriptions for proteins, glycosylated proteins, DNA and RNA, and some reorganization of the data to improve readability and interpretation. A specialized template has also been developed for reporting SAS contrast-variation data and models that incorporates the additional reporting requirements for these more complicated experiments.
The crystal structure of the self-complementary d(CGCGCG)2 Z-DNA duplex in complex with cadaverinium and potassium cations was solved at ultrahigh resolution. The oligonucleotide used for crystallization contained the enantiomeric 2′-deoxy-L-ribose instead of its natural D-enantiomer, and thus the Z-DNA duplex is right-handed.
An updated structure of adeno-associated virus serotype 4 (AAV4) is presented with a comparison to receptor-bound structures (AAV2 and AAV5) to predict why AAV4 does not bind to the adeno-associated virus receptor.
The alkaline α-galactosidase AtAkαGal3 from Arabidopsis exhibits a dual function where it can synthesize stachyose using raffinose, instead of galactinol, as the galactose donor. Crystal structures of complexes of AtAkαGal3 and its D383A mutant with various substrates and products, including galactose, galactinol, raffinose, stachyose and sucrose, reveal four complete subsites (–1 to +3) and a new secondary product-binding site, providing the first representative structure of an alkaline α-galactosidase and a model for the raffinose family of oligosaccharide synthases.
The atomic structure of a polyglycine hydrolase solved using a RoseTTAFold model-assisted molecular-replacement method reveals a two-domain enzyme. The structure reveals a novel tertiary fold and a similarity to β-lactamases.
The crystallographic structure of the DnaB·DciA complex from Vibrio cholerae reveals that the various helicase loaders share the same binding site on the bacterial replicative helicase, albeit with differences in their loading mechanisms.
A novel marine bacterial secretory phospholipase A2 (Sm-sPLA2) was characterized as being efficient in liposome biotransformation at high temperatures. The high-resolution crystal structure and mutagenesis studies revealed the determinant of the thermostability of Sm-sPLA2.