ArticleJournal of synchrotron radiation2019
Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.
Article in Journal of synchrotron radiation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Dose-dependent structural and electron-density features in the lytic polysaccharide monooxygenase NcAA9D.Acta crystallographica. Section D, Structural biology · 2026Article
- It started off as a Cys, how did it end up like this? Identifying the extent of unmodelled oxidatively modified cysteines within the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2026Article
- Coupled on-line in crystallo UV-Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins at room versus cryogenic temperature.Acta crystallographica. Section D, Structural biology · 2026Article
- Identifying and avoiding radiation damage in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2024Article
- Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source.Scientific reports · 2023Article
- Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase.Acta crystallographica. Section D, Structural biology · 2022Article
- Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.Acta crystallographica. Section D, Structural biology · 2022Article
- Quantifying and comparing radiation damage in the Protein Data Bank.Nature communications · 2022Article
- Beef tallow injection matrix for serial crystallography.Scientific reports · 2022Article
- Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis.Current opinion in structural biology · 2021Review
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Authors and funding
5 authors.
Funding
Abstract
Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.
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