4BAL | pdb_00004bal

Thaumatin from Thaumatococcus daniellii structure in complex with the europium tris-hydroxymethyltriazoledipicolinate complex at 1.30 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb4BAL/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Mutation(s): No 


• Deposited: 2012-09-14 Released: 2012-11-14 
• Deposition Author(s): Talon, R., Kahn, R., Gautier, A., Nauton, L., Girard, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.157 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

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

• PubMed: 23123834 
• DOI: https://doi.org/10.1039/c2cc36982f
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.17 kDa 
• Atom Count: 2,020 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THAUMATIN-1	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HM6	B [auth A], C [auth A], D [auth A]	4-(4-(hydroxymethyl)-1h-1,2,3-triazol-1-yl)pyridine-2,6-dicarboxylic acid C10 H8 N4 O5 JVQVNGYGRNAVBP-UHFFFAOYSA-N
EU3	E [auth A]	EUROPIUM (III) ION Eu LNBHUCHAFZUEGJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.157 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.988	α = 90
b = 57.988	β = 90
c = 150.184	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Talon, R., Kahn, R., Gautier, A., Nauton, L., Girard, E.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2015-04-01
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary