1PP3 | pdb_00001pp3

Structure of thaumatin in a hexagonal space group

• PDB DOI: https://doi.org/10.2210/pdb1PP3/pdb

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


• Deposited: 2003-06-16 Released: 2004-08-10 
• Deposition Author(s): Charron, C., Giege, R., Lorber, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Structure of thaumatin in a hexagonal space group: comparison of packing contacts in four crystal lattices.

Charron, C., Giege, R., Lorber, B.

(2004) Acta Crystallogr D Biol Crystallogr 60: 83-89

• PubMed: 14684896 
• DOI: https://doi.org/10.1107/s0907444903022613
• Primary Citation Related Structures: 
  1PP3


• PubMed Abstract: 
  

  The intensely sweet protein thaumatin has been crystallized in a hexagonal lattice after a temperature shift from 293 to 277 K. The structure of the protein in the new crystal was solved at 1.6 A resolution. The protein fold is identical to that found in three other crystal forms grown in the presence of crystallizing agents of differing chemical natures. The proportions of lattice interactions involving hydrogen bonds, hydrophobic or ionic groups differ greatly from one form to another. Moreover, the distribution of acidic and basic residues taking part in contacts also varies. The hexagonal packing is characterized by the presence of channels parallel to the c axis that are so wide that protein molecules can diffuse through them.

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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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.45 kDa 
• Atom Count: 3,479 
• Modeled Residue Count: 414 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.83	α = 90
b = 144.83	β = 90
c = 47.74	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Charron, C., Giege, R., Lorber, B.

Revision History  

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary