Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the γδ T-cell ligand T10

Abstract

T10 is a non-classical class Ib-like major histocompatibility complex (MHC) cell-surface antigen which binds directly to certain gammadelta T-cell receptors in the absence of any exogenous and endogenous ligands, such as peculiar lipids or glycolipids. The crystal structure at 2.5 A resolution of murine T10 was determined by molecular replacement using data from an almost perfectly twinned monoclinic crystal. The space group is P2(1), with unit-cell parameters a = 78.2, b = 70.0, c = 139.2 A, beta = 106.8 degrees. Self-rotation function analysis and various intensity statistics revealed the presence of pseudo-merohedral twinning, but these tests underestimated the true twin fraction of alpha approximately 0.46. Native Patterson analyses pointed to the presence of pseudo-translation among the four molecules present in the asymmetric unit. Data analysis, structure determination and model refinement are discussed.

Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase

“…Thus, twinning tests based on the cumulative intensity distribution, the |E 2 À 1| value ( Fig. 2c) or moments on intensities or structure-factor amplitudes cannot be employed, and the pseudo-translation may mask the presence of twinning (Padilla & Yeates, 2003;Rudolph et al, 2004;Zwart, GrosseKunstleve et al, 2008;Read et al, 2013). It is possible in principle that the hlFBPase data belong to Patterson symmetry P4/m with twinning emulating the higher metric symmetry P4/mmm.…”

“…In the presence of tNCS, an additional twinning test is sometimes possible (Rudolph et al, 2004). As a Patterson map of a twinned crystal contains the atomic distance information of both twin domains but no cross-peaks between them, a pseudo-translation vector in a merohedral twin should appear twice in the native Patterson map.…”

Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton

“…Two of three pseudo-cell axes coincide with a or b axis of P2 1 . The crystal also exhibits a pseudo-C222 1 lattice with cell parameters a ϭ 89.6, b ϭ 277.1, and c ϭ 78.7 Å and suggests some resemblance to the pseudomerohedral twin crystal of ␥␦ T cell ligand T10 (35). The initial phase was calculated from the multiwavelength anomalous diffraction data set of 2.4-Å resolution by treating it as P2 1 2 1 2 1 in the program SOLVE.…”

Crystallization and Preliminary Crystallographic Analysis of Laminarinase from Rhodothermus marinus: A Case of Pseudomerohedral Twinning

“…However, another fortuitous cell metric which can lead to twinning is when c cos =-a/2. This particular case of twinning has previously been observed by Declercq & Evrard [20] and Rudolph et al [21], who also performed a search in the PDB for cases where this phenomenon could have been present and was overlooked, and found several other cases with strong indications of twinning.…”

“…The twin law, -h, -k, h+l, corresponds to a two-fold rotation perpendicular to axes a and b (i.e., along c*). Rudolph et al [21] noted that, in their case, the NCS axis was parallel to the twin operation, an indication that the NCS rotation would promote twinning. In our case, however, the two molecules in the asymmetric unit are related to a 2-fold NCS axis parallel to a.…”