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.

Joanna Smietanska,Radoslaw Strzalka,Joanna Sliwiak,Mariusz Jaskolski,Janusz Wolny,Miroslaw Gilski,Zbigniew Dauter

doi:10.1107/s2059798320006841

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.

Highlights

Crystal structure modulation is classified with other aperiodic phenomena as it consists of the violation of short-range unit-cell-to-unit-cell periodicity, which over the long range is regained by a wave of structural deformations, described by an atomic modulation function (AMF)
A physical manifestation of this superstructure modulation is the fluctuation of the diffraction-pattern intensity, with strong reflections for the l index of 9n and in between at l = 9n Æ 4
The present 9Hyp/ANS structure with ninefold modulation was solved by molecular replacement (MR) using a modified Phaser algorithm that takes account of the effects of translational and rotational noncrystallographic symmetry, using the previous 7Hyp/ANS model as a probe

Summary

Introduction

Crystal structure modulation ( known as superstructure) is classified with other aperiodic phenomena as it consists of the violation of short-range unit-cell-to-unit-cell periodicity, which over the long range is regained by a wave of structural deformations, described by an atomic modulation function (AMF). In reciprocal space, this structural phenomenon is manifested by the presence of main reflections (usually stronger and affected by the modulation) arising from the (approximately periodic) main lattice of the basic unit cells and of (usually weaker) satellite reflections arising from the periodic AMF. Jeffrey Lovelace and Gloria Borgstahl have given an excellent overview of the available methods for solving problematic macromolecular crystal structures marked by order–disorder phenomena and positional modulation (Lovelace & Borgstahl, 2020)

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Conclusion