6COA

1.2 A Structure of Thaumatin Crystallized in Gel

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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

Sauter, C., Lorber, B., Giege, R.

(2002) Proteins 48: 146-150

  • DOI: 10.1002/prot.10125
  • Primary Citation of Related Structures:  

  • PubMed 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 he ...

    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.

    Related Citations: 
    • Crystallization within agarose gel in microgravity improves the quality of thaumatin crystals.
      Lorber, B.,Sauter, C.,Robert, M.C.,Capelle, B.,Giege, R.
      (1999) Acta Crystallogr. D Biol. Crystallogr. 55: 1491
    • Automatic Recognition of Ligands in Electron Density by Machine Learning.
      Kowiel, M.,Brzezinski, D.,Porebski, P.J.,Shabalin, I.G.,Jaskolski, M.,Minor, W.
      (2018) Bioinformatics --: --

    Organizational Affiliation: 

    Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thaumatin-1
A
207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Go to UniProtKB:  P02883
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA
Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.103 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.530α = 90.00
b = 58.530β = 90.00
c = 151.350γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
CNRSFrance--
Universite Louis Pasteur StrasbourgFrance--
CNES (France)France--
ESAFrance--
EU project European Bio-Crystallogenesis InitiativeFranceBIO4-CT98-0086
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection