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Preview: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography

Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



A DNA structural alphabet provides new insight into DNA flexibility
Large deformations of the DNA double helix induced by interactions with proteins and small molecules are necessary to support the biological function of DNA. Here, the software tools available at https://dnatco.org that classify the dinucleotide building blocks into 44 distinct structural classes and 11 letters of a first DNA structural alphabet are presented and are used to analyze several prototypical DNA structures.



The deduced role of a chitinase containing two nonsynergistic catalytic domains
Multiple catalytic domains in one chitinase have been shown to function synergistically during chitin degradation. Here, using biochemical and structural characterization, an insect chitinase was revealed to have two nonsynergistic catalytic domains, which may be involved in chitin synthesis instead of chitin degradation.



The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'
The structure of the folate-binding (Fol) module of Thermus thermophilus methionine synthase (MS) is described in the presence and absence of the methyltetrahydrofolate substrate. It is found that the methyltetrahydrofolate-binding environment is similar to those of previously described folate-dependent methyltransferases, highlighting the conserved role of this module in binding and perhaps activating the methyltetrahydrofolate substrate. Additionally, the structures reveal a significant difference in the C-terminal region of the T. thermophilus MS Fol module compared with other folate-binding or pterin-binding proteins.






Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 Å resolution
The crystal structure of the major outer membrane protein U (OmpU) from Vibrio cholerae has been determined, which exhibits distinct structural features from other structurally characterized porins and provides the structural basis for the bacterial invasion and phage recognition.



ARCIMBOLDO on coiled coils
The ARCIMBOLDO method of phasing through location of small fragments combined with density modification and autotracing is particularly suited for helical structures, but coiled coils remain challenging. Features designed for solving coiled coils at resolutions of up to 3 Å were tested on a pool of 150 structures.



The importance of the helical structure of a MamC-derived magnetite-interacting peptide for its function in magnetite formation
A structural change in a MamC-derived magnetite-binding peptide causes defects in its function during in vitro magnetite synthesis. Structural characterizations were conducted using X-ray crystallography and SAXS, while ITC and in vitro iron precipitation were used for functional studies.



DIALS: implementation and evaluation of a new integration package
A new X-ray diffraction diffraction data-analysis package is presented with a description of the algorithms and examples of application to biological and chemical crystallography.



Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate
The first crystal structure of Rubisco from A. thaliana is described and is compared with all other form I Rubisco crystal structures. This new structure is used to discuss the catalytic differences that could be conferred by alternative Rubisco small-subunit isoforms, and the potential benefit of differential expression of such isoforms on photosynthetic carbon assimilation in land plants.



Where is crystallography going?
Macromolecular crystallography has provided results that underpin much biological discovery and there is still scope for further development; however, a revolution in electron imaging now means that it can also routinely provide detailed atomic-level descriptions. This article attempts to tease out where crystallography is going and consider what its place might be in the new landscape.



CCP4i2 – the new graphical user interface to the CCP4 program suite
CCP4i2 is a graphical user interface to the CCP4 (Collaborative Computational Project, Number 4) software suite and a Python language framework for software automation.



An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features
Experimental phasing of macromolecular crystals is described and explained, with the emphasis on its implementation in the programs SHELXC, SHELXD and SHELXE, which are also used in a number of macromolecular structure-solution pipelines.



Distributed computing for macromolecular crystallography
The paper describes recent CCP4 initiatives and projects aimed at bringing software and data services which utilize distributed computational resources to users.



Substructure determination using phase-retrieval techniques
The relaxed averaged alternating reflections (RAAR) phase-retrieval method has been applied to crystallography for the first time and has been shown to outperform charge flipping in anomalous substructure determination.



Maximum-likelihood determination of anomalous substructures
Likelihood-based SAD substructure determination can be initiated using a fast translation-search algorithm based on a linear approximation to the SAD likelihood target, followed by log-likelihood-gradient map completion.



Macromolecular refinement by model morphing using non-atomic parameterizations
A method is described for the refinement of an electron-density model against a set of structure-factor observations which does not rely on atomic parameters. The effective level of detail in the parameterization can be varied to ensure that the refinement is well determined at any resolution supported by the data.