issue contents

Journal logoSTRUCTURAL
ISSN: 2059-7983

September 2016 issue

Highlighted illustration

Cover illustration: Use of the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding of macromolecules. iMDFF has been used to individually correct and re-refine three structures and strategies for working with such challenging data sets are suggested (Croll & Andersen, p. 1006). Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement. This image gives an overview of the C4 structure and the key corrections made in this study. Register errors affecting two [beta]-strands and a poorly ordered loop in the MG3 domain (marked with an asterisk) and four [beta]-strands in the CUB domain (marked with a dagger) were corrected with shifts of 1-3 residues. All C[alpha] atoms which shifted by more than 2.5 Å are shown in sphere representation and coloured according to the distance moved. Additionally, four low-occupancy trimethyllead ions were resolved (black spheres and arrowheads) as well as the O-linked N-acetylgalactosamine (arrow; obscured behind protein in this image).

research papers

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The first interpretable X-ray scattering data concerning lateral (radial) packing of bone collagen molecules is presented, which indicates that bone contains spatially discrete collagen microfibrils. A spatially discrete microfibril model supports structure–function-based explanations for internal fibril mineralization and for the unique pattern of collagen post-translational modifications in mineralized tissues.

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Crystal structures of the metallochaperone CopM from Synechocystis sp. PCC 6803 have been solved at 1.45–2.5 Å resolution, including apo, Cu+-bound, Ag+-bound and Cu2+-bound forms. A previously functionally unknown domain was found to contain a conserved copper/silver-binding motif.

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An interactive molecular-dynamics environment allows significantly improved results when rebuilding macromolecular structures into low-resolution maps. Corrections are presented to three existing structures of complement C4 in distinct functional states, all with MolProbity scores of <2 despite having resolutions lower than 3.5 Å.

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The structure of the extracellular portion of interferon-γ receptor 2, a member of the class II cytokine receptors, has been solved. Bioinformatic analysis revealed independent evolutionary behaviour of both receptor domains and identified a putative binding site for interferon-γ.

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A genetic algorithm is described and used to select which sub-data sets from a larger pool can be merged into a high-quality data set.

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The first crystal structures of a dimeric, cold-adapted β-D-galactosidase from Paracoccus sp. 32d and its complex with galactose were determined. The atypical arrangement of domains may be one of the factors that are responsible for the creation of a functional dimer of this enzyme.

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A method for the more accurate refinement of small molecules and ligands in biomolecular structures is provided. Improved ligand geometry is obtained via an all-atom molecular-mechanics force field.

addenda and errata

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Some key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models described in the article by Urzhumtsev et al. [(2015) Acta Cryst. D71, 1668–1683] are clarified and developed, and a reference on a wrong model is corrected.

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