Arginine off-kilter: guanidinium is not as planar as restraints denote

The geometry of arginine shows more complexity than is accommodated by the standard restraints.

High-performance macromolecular data delivery and visualization for the web

This article provides a survey of available web services and tools for data delivery and visualization of macromolecular structures.

Semi-empirical model to estimate ideal conditions for the growth of large protein crystals

A semi-empirical model to estimate the optimum conditions for the growth of large protein crystals has been developed.

Real-space quantum-based refinement for cryo-EM: Q|R#3

The implementation of quantum-based real-space refinement in qr.refine is described.

Shift-field refinement of macromolecular atomic models

Shift-field refinement is an approach to the refinement of a model against a set of structure-factor observations which is not tied to an underlying atomic parameterization. The performance of the method is evaluated for the refinement of positional parameters over a set of 452 molecular-replacement problems.

The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family

AjiA1 is an adenylate-forming enzyme (AFE) family member that catalyzes the condensation of two molecules of 3-hydroxyanthranilic acid using ATP as a co-substrate. The structure of AjiA1 in its apo form was solved and revealed key conformational changes, including an unusual loop swapping, suggesting that it should be classified into a new AFE subgroup.

Influence of the presence of the heme cofactor on the JK-loop structure in indole­amine 2,3-dioxygenase 1

This article provides an in-depth analysis of structural aspects of the heme-bound structure of indoleamine 2,3-dioxygenase 1 with a complete refined JK-loop (the overall crystal structure, the quality of the structure, the dimerization interfaces and an analysis of the JK-loop conformation) followed by a molecular-dynamics study of the influence of heme occupation on the conformation of the JK-loop.

The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography

A novel three-residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described.

Structural variability of CG-rich DNA 18-mers accommodating double T–T mismatches

Two investigated DNA 18-mers indicate a dynamic equilibrium of conformations in solution and crystallize as duplexes with two consecutive T–T mismatches. Neither these mismatched nucleotides nor others found in the PDB exhibit unique structural features compared with Watson–Crick paired nucleotides.

Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis

Structural studies of glycoproteins are often complicated by glycan complexity. Here, it is shown that the GlycoDelete HEK293 cell line engineered to produce glycan stumps produces homogeneous glycoproteins that are ideal for crystallogenesis and other structural studies.

Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-keto­decanoyl-CoA: capturing active and inactive states of its hydratase and de­hydrogenase catalytic sites

The 1.7 Å resolution crystal structure of peroxisomal multifunctional enzyme type 1 (MFE1) shows a conformation in which both catalytic sites are noncompetent. An analysis of the structures of its complexes with 3-ketodecanoyl-CoA suggests how conformational flexibility of MFE1 could be important for its function.

Low-resolution structures of modular nanotransporters shed light on their functional activity

Artificial multifunctional polypeptide constructs (modular nanotransporters, MNTs) have great potential in the treatment of various diseases, particularly cancer. In this study, a low-resolution 3D structure of an MNT in solution was obtained by atomic force microscopy, transmission electron microscopy and small-angle X-ray scattering coupled to size-exclusion chromatography.