6SJJ

A new modulated crystal structure of ANS complex of St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell

Summary for 6SJJ

• Entry DOI: 10.2210/pdb6sjj/pdb
• Descriptor: PR-10 protein, 8-ANILINO-1-NAPHTHALENE SULFONATE, SULFATE ION, ... (7 entities in total)
• Functional Keywords: plant protein, plant hormone binding, phytohormone binding, cytokinin, plant defense, pathogenesis-related protein, pr-10 protein, hypericin, depression, pr-10 fold, hydrophobic cavity, glycine-rich loop, ans displacement assay (ada), commensurately modulated superstructure, tetartohedral twinning
• Biological source: Hypericum perforatum (St. John's wort)
• Total number of polymer chains: 36
• Total formula weight: 709450.37

Authors

Smietanska, J.,Sliwiak, J.,Gilski, M.,Dauter, Z.,Strzalka, R.,Wolny, J.,Jaskolski, M. (deposition date: 2019-08-13, release date: 2020-06-24, Last modification date: 2024-01-24)

Primary citation

Smietanska, J.,Sliwiak, J.,Gilski, M.,Dauter, Z.,Strzalka, R.,Wolny, J.,Jaskolski, M.
A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell.
Acta Crystallogr D Struct Biol, 76:653-667, 2020

PubMed Abstract: Superstructure modulation, with violation of the strict short-range periodic order of consecutive crystal unit cells, is well known in small-molecule crystallography but is rarely reported for macromolecular crystals. To date, one modulated macromolecular crystal structure has been successfully determined and refined for a pathogenesis-related class 10 protein from Hypericum perforatum (Hyp-1) crystallized as a complex with 8-anilinonaphthalene-1-sulfonate (ANS) [Sliwiak et al. (2015), Acta Cryst. D71, 829-843]. The commensurate modulation in that case was interpreted in a supercell with sevenfold expansion along c. When crystallized in the additional presence of melatonin, the Hyp-1-ANS complex formed crystals with a different pattern of structure modulation, in which the supercell shows a ninefold expansion of c, manifested in the diffraction pattern by a wave of reflection-intensity modulation with crests at l = 9n and l = 9n ± 4. Despite complicated tetartohedral twinning, the structure has been successfully determined and refined to 2.3 Å resolution using a description in a ninefold-expanded supercell, with 36 independent Hyp-1 chains and 156 ANS ligands populating the three internal (95 ligands) and five interstitial (61 ligands) binding sites. The commensurate superstructures and ligand-binding sites of the two crystal structures are compared, with a discussion of the effect of melatonin on the co-crystallization process.

PubMed: 32627738
DOI: 10.1107/S2059798320006841

Experimental method

X-RAY DIFFRACTION (2.3 Å)