PDBsum entry 2plh

Toxin

PDB id: 2plh

Contents

Protein chain

45 a.a. *

Ligands

ACT ×3

PO4

SBT ×2

GOL ×2

Waters ×108

* Residue conservation analysis

PDB id:

2plh

Name:

Toxin

Title:

Structure of alpha-1-purothionin at room temperature and 2.8 angstroms resolution

Structure:

Alpha-1-purothionin. Chain: a. Other_details: solute molecules not added to the

Source:

Triticum aestivum. Bread wheat. Organism_taxid: 4565. Tissue: grain

Resolution:

2.50Å R-factor: 0.155

Authors:

M.M.Teeter,B.Stec,U.Rao

Key ref:

U.Rao et al. (1995). Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 1: alpha1-purothionin revisited. Acta Crystallogr D Biol Crystallogr, 51, 904-913. PubMed id: 15299760 DOI: 10.1107/S0907444995002964

Date:

09-Jul-93 Release date: 03-Apr-96

Protein chain

P01544  (THN1_WHEAT) -  Alpha-1-purothionin (Fragment) from Triticum aestivum

Seq: 126 a.a.

Struc: 45 a.a.

DOI no: 10.1107/S0907444995002964

Acta Crystallogr D Biol Crystallogr 51:904-913 (1995)

PubMed id: 15299760

Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 1: alpha1-purothionin revisited.

U.Rao, B.Stec, M.M.Teeter.

ABSTRACT

The three-dimensional structure of alpha(1)-purothionin (alpha(1)-PT), a wheat-germ protein and a basic lytic toxin, was previously solved by molecular-replacement methods using an energy-minimized predicted model and refined to an R-factor of 21.6% [Teeter, Ma, Rao & Whitlow (1990). Proteins Struct. Funct. Genet. 8, 118-1321. Some deficiencies of the model motivated us to revisit the structure and to continue the refinement. Here we report a significantly improved structure refined to an R-factor of 15.5% with excellent geometry. The refinement of this relatively low resolution structure ( approximately 2.8 A) is well suited to test the limitations of classical methods of refinement and to address the problem of overfitting, The final structure contains 434 atoms including 330 protein atoms, 70 waters, three acetates, two glycerols, one sec-butanol and one phosphate. The key solute molecules (acetate ion and phosphate ion) play a crucial role in the lattice formation. Phosphate and glycerol found in the structure may be important for biological activity of the toxins.

Selected figure(s)

Figure 4.
Fig. 4. (a) A disordered CA molecule modeled at special position I I(i,0,~) superimposed on the corresponding 2F o -F C density (solid lines). Alo superimpsed is the negative difference Fourier map (contoured at 2c~ level, in broken lines), indicating the absence of methyl plane. View shown is the prjection down the [110] axis. (b) A 90 ° rotated view of the similar map from the latr refined model, showing the diordered acetates at the special position making good interaction wit four symmetry-related Asn ll residues.

Figure 6.
Fig. 6. se of an OMIT map for Argl9. a) 2Fo - Fc map (solid lines) around Argl9 before the OMIT map, showing the poor density for the side chain. Both 2Fo- Fc map and F,,- Fc map (broken lines) with the side chain omitted are indicative of a new conformation for this residue. (b) 2Fo- F,. map supeimposed on Argl9 modeled in a new conformation in the final model.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 904-913) copyright 1995.

Figures were selected by an automated process.