April 2023 issue
Room-temperature biological crystallography has seen a resurgence in recent years and a collection of articles recently published in IUCrJ, Acta Cryst. D Structural Biology and Acta Cryst. F Structural Biology Communications, have been collected together to produce a virtual special issue at https://journals.iucr.org/special_issues/2022/RT/.
Likelihood-based rotation, translation and refinement targets have been derived for docking models into cryo-EM reconstructions.
Exploiting analogies to crystallographic molecular replacement, a strategy for docking into cryo-EM maps is informed by the calculation of expected log-likelihood-gain scores.
Ambient temperature structures of B. longum phosphoketolase holoenzyme and its complex with a putative inhibitor, phosphoenolpyruvate, demonstrated striking conformational change of the loop at the entrance to the active-site pocket compared with known cryogenic temperature phosphoketolase structures. This structural change highlighted the reaction mechanism and substrate specificity of this enzyme.
Fragment derivatives occupy diverse binding sites in two crystal forms of the RNA helicase BRR2 that coincide with predicted, conformation-dependent ligand hot spots.
L-Proline trans-hydroxylase and its complexes with substrate and product reveal the structural basis of trans–cis proline hydroxylation selectivity. Structure-based sequence alignment and structural comparison suggest signatures for in-line or off-line AKG-binding modes in AKG-dependent hydroxylases and provide deeper insight into AKG-dependent hydroxylation.
A neural network trained to identify unfavourable fragments and therefore improve protein model building in the Buccaneer software is described.
A new equation for the calculation of substructure-factor amplitudes for substructure detection from a single-wavelength anomalous diffraction experiment produces better results compared with the currently used estimates in test cases.
The crystal structure of the electron transfer complex between arsenite oxidase (AioAB) from Pseudorhizobium banfieldiae sp. strain NT-26 and its native electron acceptor cytochrome c552 (cytc552) is presented. Cytc552 docks within a cleft at the interface of the AioA and AioB subunits, which allows a close association between redox cofactors.; this close association presumably facilitates fast electron transfer and underpins the ability of this organism to respire in arsenic contaminated environments.
addenda and errata
The article by Barbarin-Bocahu & Graille [(2022), Acta Cryst. D78, 517–531] is corrected.