Dissecting random and systematic differences between noisy composite data sets

A multidimensional scaling analysis of pairwise correlation coefficients is presented which positions data sets in a sphere with unit radius of an abstract, low-dimensional space at radii inversely proportional to their levels of random error and at spherical angles related to their mutual systematic differences. This reduction in dimensionality can not only be used for classification purposes, but also to derive data-set relations on a continuous scale.

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

The structure of an Hfq homolog from the deep-branching thermophilic bacterium Aquifex aeolicus, determined to 1.5 Å resolution both in the apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer.

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Using all available metal-containing organic compound structures in the Cambridge Structural Database, a novel data-driven method to derive bond-valence R₀ parameters was developed. While confirming almost all reference literature values, two distinct populations of Fe^II—N and Fe^III—N bonds are observed, which are interpreted as low-spin and high-spin states of the coordinating iron. Based on the R₀ parameters derived here, guidelines for the modeling of iron–ligand distances in macromolecular structures are suggested.

Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei

This study of shrimp thioredoxin sheds new light on the existence of monomeric and dimeric populations in solution. It is demonstrated that the Cys73 residue is essential for dimer formation and that the Cys73Ser mutant has the same activity as the wild type.

Crystal structures of human 3-hydroxyanthranilate 3,4-dioxygenase with native and non-native metals bound in the active site

Two structures of human 3-hydroxyanthranilate 3,4-dioxygenase, one with iron bound at the active site and one with zinc bound at the active site, are reported.

Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association

In eight of the nine crystal structures of M. smegmatis MutT1 reported here, an arrangement is observed in which domain 1 of one molecule and domain 2 of a neighbouring molecule (trans domain 2) are brought into close proximity, with ligand-binding sites at the interface between the two domains. This and other structural observations, along with biochemical results, lead to a plausible proposal for the mechanism of action of the enzyme.

Crystal structures of Hsp104 N-terminal domains from Saccharomyces cerevisiae and Candida albicans suggest the mechanism for the function of Hsp104 in dissolving prions

The crystal structures of Hsp104 N-terminal domains from S. cerevisiae (ScHsp104NTD) and C. albicans (CaHsp104NTD) were determined to high resolution. The structures of ScHsp104NTD and CaHsp104NTD reveal that the yeast Hsp104 N-terminal domain may utilize a conserved putative peptide-binding groove to interact with misfolded polypeptides.

Low-dose fixed-target serial synchrotron crystallography

A time- and sample-efficient approach for the serial collection of room-temperature diffraction data using a fixed target at a synchrotron is demonstrated.

`Atomic resolution': a badly abused term in structural biology

The term `atomic resolution' is very often abused in presenting macromolecular structures.

Responses to `Atomic resolution': a badly abused term in structural biology

Responses to the letter to the editor `Atomic resolution': a badly abused term in structural biology [Wlodawer & Dauter (2017), Acta Cryst. D73, 379–380].

Free Radicals in Biology and Medicine. Fifth Edition

Metallomics. A Primer of Integrated Biometal Sciences