PDBsum entry: 1wgt

Lectin (agglutinin)

PDB-id: 1wgt

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

171 a.a. *

Waters ×358

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1wgt

Name:

Lectin (agglutinin)

Title:

X-ray structure of wheat germ agglutinin isolectin 3

Structure:

Wheat germ lectin. Chain: a, b. Engineered: yes

Source:

Triticum aestivum. Bread wheat. Organism_taxid: 4565

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: P10969 (AGI3_WHEAT)

Seq:

186 a.a.

Struc:

171 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

1.90Å

R-factor:

0.191

Authors:

K.Harata,H.Nagahora,Y.Jigami

Key ref:

K.Harata et al. (1995). X-ray structure of wheat germ agglutinin isolectin 3.. Acta Crystallogr D Biol Crystallogr, 51, 1013-1019. [PubMed id: 15299769] [DOI: 10.1107/S0907444995004070]

Date:

17-Apr-95

Release date:

10-Jul-95

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1107/S0907444995004070

Acta Crystallogr D Biol Crystallogr 51:1013-1019 (1995)

PubMed id: 15299769

X-ray structure of wheat germ agglutinin isolectin 3.

K.Harata, H.Nagahora, Y.Jigami.

ABSTRACT

Wheat germ agglutinin isolectin 3 (WGA3) was crystallized from 10 mM acetate buffer at pH 4.9 containing 6 mM CaCl(2) and 4%(v/v) ethanol. The crystal belongs to monoclinic space group P2(1) with unit-cell dimensions a = 44.86, b = 91.02, c = 44.86 A, and beta = 110.22 degrees. The asymmetric unit contains two molecules (V(m) = 2.51 A(3) Da(-1)). The crystal structure was solved by the molecular-replacement method and was refined by the simulated-annealing method. in the resolution range 8-1.9 A. The r.m.s. deviations from the ideal bond distances and angles were 0.014 A, and 3.0 degrees, respectively, and the estimated coordinate error was 0.2-0.25 A. The two molecules in the asymmetric unit are related by the pseudo twofold symmetry and form a dimer structure. The backbone structures of the two subunits are nearly identical with the r.m.s. difference of 0.36 A for the superposition of equivalent C(alpha) atoms. The dimer structure is very similar to those of isolectins 1 and 2 with the r.m.s. difference of 0.35-0.39 A for the C(alpha) superposition. Since amino-acid residues which differ from those of isolectin 1 or 2 are not involved in the contact between the two subunits, the subunit-subunit interaction is not significantly affected by the replacement of these residues. As a result, the geometry of the sugar-binding sites which are located at the interface between the two subunit molecules is basically conserved among three isolectins.

Selected figure(s)

Figure 6.
Fig. 6. Plot of temperature factors averaged for main-chain peptide and side-chain groups in molecule 1 against residue number. ~

Figure 8.
Fig. 8. Stereoview of the structure of the primary sugar-binding site. The corre- sponding region of WGA1 is superim- posed and shown by thin lines. Amino- acid residues in molecules 1 and 2 are designated as A and B, respectively.

Figure 9.
Fi. 9. Crystal structure viewed long the b axis. The C a atoms of molecule I is shown by circles ad molecule 2 is drawn with thin lines.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 1013-1019) copyright 1995.

Figures were selected by an automated process.