Implications of AlphaFold2 for crystallographic phasing by molecular replacement

The implications of the AlphaFold2 protein structure-modelling software for crystallographic phasing strategies are discussed.

Best practices for time-resolved serial synchrotron crystallography

The key factors that should be considered during the planning and execution of a time-resolved crystallographic experiment are discussed, with a focus on time-resolved serial synchrotron crystallography.

X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure

A quinary multi-hexameric helical structure of T. cruzi NDPK1 is supported by crystallographic and in vivo studies.

A radical approach to radicals

New restraints for the nitroxide radical ligand MTN defined based on quantum-chemical computations allow the accurate re-refinement of protein structures.

Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts

High-resolution X-ray diffraction data were collected at room temperature for light- and dark-adapted states of the archaerhodopsin-3 photoreceptor using transparent and opaque polymer-film sample mounts.

Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2

In this study, the crystal structure of anti-CRISPR-associated 2 (Aca2) was solved and it was shown that Aca2 forms dimers in solution, which are critical for promoter binding; specific residues that are critical for DNA binding and their conservation were revealed. Since the mechanism of action is largely conserved among different Aca protein families, insights are provided into their structure and function.

B-factor accuracy in protein crystal structures

The accuracy of B factors, estimated by comparing the same atoms in numerous protein crystal structures, is rather modest: close to 9 Ų in ambient-temperature structures and to 6 Ų in low-temperature structures. These values are similar to those estimated two decades ago, indicating that little has changed since.

Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA

The binding properties of two drug-like fragments to a conformationally dynamic site in disulfide bond-forming protein A from B. pseudomallei are described.

Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation

Contrary to expectation from orthologous structures from mouse and cow, a structure of holo human adenosine deaminase 1 shows that it adopts a closed conformation at the entry to its active site. This finding poses a cautionary tale for reliance on homologs to make structural inferences relevant to applications such as protein engineering or drug development.

Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering

The crystal structure of YxaL was determined, revealing an eight-bladed β-propeller fold with structural variations. The protein was subsequently engineered based on the structure, resulting in an improved plant growth-promoting activity.

CryoEM analysis of small plant biocatalysts at sub-2 Å resolution

Although cryo-electron microscopy has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes so far remains largely unexplored. Here, two cryo-EM structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution are reported.

A case for glycerol as an acceptable additive for single-particle cryoEM samples

It is shown that the inclusion of glycerol in single-particle cryoEM buffers does not preclude high-resolution structure determination, as demonstrated by an ∼2.3 Å resolution reconstruction of mouse apoferritin (∼500 kDa) and an ∼3.3 Å resolution reconstruction of rabbit muscle aldolase (∼160 kDa) in the presence of 20%(v/v) glycerol.