1LXZ | pdb_00001lxz

Structure of thaumatin crystallized in the presence of glycerol

• PDB DOI: https://doi.org/10.2210/pdb1LXZ/pdb

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


• Deposited: 2002-06-06 Released: 2003-01-14 
• Deposition Author(s): Charron, C., Kadri, A., Robert, M.C., Giege, R., Lorber, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.195 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin.

Charron, C., Kadri, A., Robert, M.C., Giege, R., Lorber, B.

(2002) Acta Crystallogr D Biol Crystallogr 58: 2060-2065

• PubMed: 12454465 
• DOI: https://doi.org/10.1107/s0907444902017183
• Primary Citation Related Structures: 
  1LXZ, 1LY0


• PubMed Abstract: 
  

  The intensely sweet protein thaumatin has been crystallized at 293 K in the presence of sodium tartrate and 25%(v/v) glycerol for X-ray diffraction data collection at 100 K. A comparison of the three-dimensional structure model derived from a crystal grown in the presence of glycerol with that of a control deprived of this additive reveals only minor changes in the overall structure but a approximately 20% reduction in the number of water molecules. X-ray topography analyses show that the overall quality of the crystals prepared in the presence of this cryoprotectant is enhanced.

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Organizational Affiliation: 
• Département 'Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse' UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15Rue René Descartes, F-67084 Strasbourg Cedex, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.38 kDa 
• Atom Count: 1,821 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.195 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.801	α = 90
b = 57.801	β = 90
c = 149.96	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Charron, C., Kadri, A., Robert, M.C., Giege, R., Lorber, B.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary