6QRZ

Crystal structure of R2-like ligand-binding oxidase from Sulfolobus acidocaldarius solved by 3D micro-crystal electron diffraction

Summary for 6QRZ

• Entry DOI: 10.2210/pdb6qrz/pdb
• Descriptor: Ribonucleoside-diphosphate reductase, MANGANESE (III) ION, FE (III) ION (3 entities in total)
• Functional Keywords: micro-crystal, microed, r2-like ligand-binding oxidase, mn/fe cofactor, ribonucleotide reductase r2 subunit fold, metalloprotein oxidoreductase, ferritin-like superfamily, oxidoreductase
• Biological source: Sulfolobus acidocaldarius DSM 639
• Total number of polymer chains: 1
• Total formula weight: 38169.40

Authors

Xu, H.,Lebrette, H.,Clabbers, M.T.B.,Zhao, J.,Griese, J.J.,Zou, X.,Hogbom, M. (deposition date: 2019-02-20, release date: 2019-04-24, Last modification date: 2024-05-15)

Primary citation

Xu, H.,Lebrette, H.,Clabbers, M.T.B.,Zhao, J.,Griese, J.J.,Zou, X.,Hogbom, M.
Solving a new R2lox protein structure by microcrystal electron diffraction.
Sci Adv, 5:eaax4621-eaax4621, 2019

PubMed Abstract: Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

PubMed: 31457106
DOI: 10.1126/sciadv.aax4621

Experimental method

ELECTRON CRYSTALLOGRAPHY (3 Å)