PDBsum entry: 1kwn

Plant protein

PDB id: 1kwn

Contents

Protein chain

207 a.a. *

Ligands

TAR

Waters ×197

* Residue conservation analysis

PDB id:

1kwn

Name:

Plant protein

Title:

1.2 a structure of thaumatin crystallized in gel

Structure:

Thaumatin i. Chain: a

Source:

Thaumatococcus daniellii. Miracle fruit. Organism_taxid: 4621. Other_details: purchased by sigma (cat. No. T7638)

Biol. unit:

Dimer (from PQS)

Resolution:

1.20Å R-factor: 0.128 R-free: 0.145

Authors:

C.Sauter,B.Lorber,R.Giege

Key ref:

C.Sauter et al. (2002). Towards atomic resolution with crystals grown in gel: the case of thaumatin seen at room temperature. Proteins, 48, 146-150. PubMed id: 12112683 DOI: 10.1002/prot.10125

Date:

30-Jan-02 Release date: 11-Dec-02

Protein chain

P02883  (THM1_THADA) -  Thaumatin-1

Seq: 207 a.a.

Struc: 207 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasmic vesicle (2 terms)

DOI no: 10.1002/prot.10125

Proteins 48:146-150 (2002)

PubMed id: 12112683

Towards atomic resolution with crystals grown in gel: the case of thaumatin seen at room temperature.

C.Sauter, B.Lorber, R.Giegé.

ABSTRACT

One reason for introducing a gel in the crystallization medium of proteins is its ability to reduce convection in solution. This can lead to better nucleation and growth conditions, and to crystals having enhanced diffraction properties. We report here the X-ray characterization at room temperature of high-quality crystals of the intensely sweet thaumatin prepared in a sodium tartrate solution gelified with 0.15% (m/v) agarose. Using a synchrotron radiation, these crystals diffracted to a previously unachieved resolution. A diffraction dataset was collected from four crystals at a resolution of 1.2 A with a R(sym) of 3.6% and a completeness of 99%. Refinement was carried out to a final crystallographic R-factor of 12.0%. The quality of the electron density map allowed for the observation of fine structural details in the protein and its solvation shell. Crystallization in gel might be used more generally to improve the quality of macromolecular crystals. Advantages provided by the gelified medium in the frame of structural studies are emphasized.

Selected figure(s)

Figure 1.
Figure 1. High-quality crystals yield high-quality electron density maps. A: An almost perfect bipyramidal crystal of thaumatin (1 mm in length) with bright birefringence colors grown in 0.15% (m/v) agarose gel. B: Detail of the electron density map showing an ion of tartrate, the crystallizing agent, that connects three symmetry-related thaumatin molecules in the crystal lattice. Dashed lines highlight the main interactions between the tartrate molecule and protein residues. They consist of either salt bridges or hydrogen bonds (mostly mediated by a water molecule) with distances varying between 2.47 and 3.05 Å; they involve Arg29 and Ser36 of a first monomer (bottom), Tyr157, Tyr169 and Thr154 of a second (left), and Pro141 of a third molecule (top right). The 3F[o]-2F[c] Fourier map is contoured at a level of 1.8 .

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2002, 48, 146-150) copyright 2002.