1DGW

Structure of the rhombohedral crystal of canavalin from jack bean

Summary for 1DGW

• Entry DOI: 10.2210/pdb1dgw/pdb
• Related: 1CAW 1CAX 1DGR 2CAU 2CAV
• Descriptor: CANAVALIN, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: duplicated swiss-roll beta barrels, loops with alpha helices, merohedral/ hemihedral twinning, plant protein
• Biological source: Canavalia ensiformis (jack bean); More
• Total number of polymer chains: 3
• Total formula weight: 40077.94

Authors

Ko, T.-P.,McPherson, A. (deposition date: 1999-11-26, release date: 1999-12-20, Last modification date: 2024-02-07)

Primary citation

Ko, T.P.,Kuznetsov, Y.G.,Malkin, A.J.,Day, J.,McPherson, A.
X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin.
Acta Crystallogr.,Sect.D, 57:829-839, 2001

PubMed Abstract: The structure of canavalin, the vicilin-class storage protein from jack bean, was refined to 1.7 A resolution in a highly twinned rhombohedral crystal of space group R3 and unit-cell parameters a = b = c = 83.0 A, alpha = beta = gamma = 111.1 degrees. The resulting R and R(free) were 0.176 and 0.245, respectively. The orthorhombic crystal structure (space group C222(1), unit-cell parameters a = 136.5, b = 150.3, c = 133.4 A) was also refined with threefold non-crystallographic symmetry restraints. R and R(free) were 0.181 and 0.226, respectively, for 2.6 A resolution data. No significant difference in the protein structure was seen between these two crystal forms, nor between these two and the hexagonal and cubic crystal forms reported elsewhere [Ko et al. (1993), Acta Cryst. D49, 478-489; Ko et al. (1993), Plant Physiol. 101, 729-744]. A phosphate ion was identified in the lumen of the C-terminal beta-barrel. Lattice interactions showed that the trimeric molecule could be well accommodated in both 'top-up' and 'bottom-up' orientations in a rhombohedral unit cell of the R3 crystal and explained the presence of a high twin fraction. The large inter-trimer stacking interface of the C222(1) crystal may account for its relative stability. Atomic force microscopy (AFM) investigations of the growth of three crystal forms of canavalin indicate the rhombohedral form to be unique. Unlike the other two crystal forms, it contains at least an order of magnitude more screw dislocations and stacking faults than any other macromolecular crystal yet studied, and it alone grows principally by generation of steps from the screw dislocations. The unusually high occurrence of the screw dislocations and stacking faults is attributed to mechanical stress produced by the alternate molecular orientations in the rhombohedral crystals and their organization into discrete domains or blocks. At boundaries of alternate domains, lattice strain is relieved by the formation of the screw dislocations.

PubMed: 11375502
DOI: 10.1107/S0907444901003791

Experimental method

X-RAY DIFFRACTION (1.7 Å)