4BAR

Thaumatin from Thaumatococcus daniellii structure in complex with the europium tris-hydroxyethyltriazoledipicolinate complex at 1.20 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.155 (Depositor), 0.149 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.132 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IKXClick on this verticalbar to view details

This is version 2.3 of the entry. See complete history


Literature

Clicked europium dipicolinate complexes for protein X-ray structure determination.

Talon, R.Nauton, L.Canet, J.L.Kahn, R.Girard, E.Gautier, A.

(2012) Chem Commun (Camb) 48: 11886-11888

  • DOI: https://doi.org/10.1039/c2cc36982f
  • Primary Citation of Related Structures:  
    4BAD, 4BAF, 4BAL, 4BAP, 4BAR

  • PubMed Abstract: 

    New trisdipicolinic acid-lanthanide complexes are reported as phasing agents for X-ray crystallography of proteins. It is demonstrated that CuAAC modifications allow protein co-crystallization with low concentration of lanthanide complexes leading to an accurate structure determination.


  • Organizational Affiliation

    CEA, DSV, Institut de Biologie Structurale (IBS), 41 rue Jules Horowitz, Grenoble F-38027, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THAUMATIN-1207Thaumatococcus danielliiMutation(s): 0 
UniProt
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.155 (Depositor), 0.149 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.132 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.852α = 90
b = 57.852β = 90
c = 150.215γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IKXClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-11-28
    Changes: Database references, Derived calculations
  • Version 1.2: 2015-03-18
    Changes: Database references
  • Version 1.3: 2015-03-25
    Changes: Database references
  • Version 2.0: 2018-04-11
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2018-12-19
    Changes: Data collection, Database references, Derived calculations
  • Version 2.2: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 2.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary