Thaumatin from Thaumatococcus Danielli in complex with tris-dipicolinate Europium

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.

Pompidor, G.Maury, O.Vicat, J.Kahn, R.

(2010) Acta Crystallogr D Biol Crystallogr 66: 762-769

  • DOI: https://doi.org/10.1107/S0907444910010954
  • Primary Citation of Related Structures:  
    2PE7, 2PES, 3LGR

  • PubMed Abstract: 

    Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic elastase and xylanase from Trichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinic C2 crystal form that diffracted to high resolution.

  • Organizational Affiliation

    Institut de Biologie Structurale J.-P. Ebel, UMR 5075, 41 Rue Jules Horowitz, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Preprothaumatin I207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Explore P02883 
Go to UniProtKB:  P02883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02883
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.55α = 90
b = 57.55β = 90
c = 149.4γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
BM30Adata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description