2VHK

Atomic resolution (0.94 A) structure of purified thaumatin I grown in sodium L-tartrate at 22C

• PDB DOI: https://doi.org/10.2210/pdb2VHK/pdb

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


• Deposited: 2007-11-21 Released: 2009-02-10 
• Deposition Author(s): Jakoncic, J., Asherie, N., Ginsberg, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.134 
• R-Value Work: 0.124 
• R-Value Observed: 0.125 

Starting Model: experimental

Literature

Tartrate Chirality Determines Thaumatin Crystal Habit

Asherie, N., Jakoncic, J., Ginsberg, C., Greenbaum, A., Stojanoff, V., Hrnjez, B.J., Blass, S., Berger, J.

(2009) Cryst Growth Des 9: 4189

• DOI: https://doi.org/10.1021/CG900465H

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.73 kDa 
• Atom Count: 2,148 
• Modelled Residue Count: 206 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THAUMATIN-I	A	206	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
TLA	E [auth A], F [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.134 
• R-Value Work: 0.124 
• R-Value Observed: 0.125 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.88	α = 90
b = 57.88	β = 90
c = 149.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Jakoncic, J., Asherie, N., Ginsberg, C.

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description