5AVG

The 0.95 angstrom structure of thaumatin crystallized in high-strength agarose hydrogel

• PDB DOI: https://doi.org/10.2210/pdb5AVG/pdb

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


• Deposited: 2015-06-16 Released: 2015-07-08 
• Deposition Author(s): Sugiyama, S., Shimizu, N., Maruyama, M., Sazaki, G., Hirose, M., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H.
• Funding Organization(s): JSPS KAKENHI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.144 
• R-Value Work: 0.127 
• R-Value Observed: 0.128 

Starting Model: experimental

Literature

Growth of protein crystals in hydrogels prevents osmotic shock

Sugiyama, S., Maruyama, M., Sazaki, G., Hirose, M., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H.

(2012) J Am Chem Soc 134: 5786-5789

• PubMed: 22435400 
• DOI: https://doi.org/10.1021/ja301584y
• Primary Citation of Related Structures:  
  5AVD, 5AVG, 5AVH, 5AVN


• PubMed Abstract: 
  

  High-throughput protein X-ray crystallography offers a significant opportunity to facilitate drug discovery. The most reliable approach is to determine the three-dimensional structure of the protein-ligand complex by soaking the ligand in apo crystals. However, protein apo crystals produced by conventional crystallization in a solution are fatally damaged by osmotic shock during soaking. To overcome this difficulty, we present a novel technique for growing protein crystals in a high-concentration hydrogel that is completely gellified and exhibits high strength. This technique allowed us essentially to increase the mechanical stability of the crystals, preventing serious damage to the crystals caused by osmotic shock. Thus, this method may accelerate structure-based drug discoveries.

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Organizational Affiliation: 

Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.16 kDa 
• Atom Count: 2,034 
• Modelled Residue Count: 206 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin-1	A	206	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: 0.95 Å
• R-Value Free: 0.144 
• R-Value Work: 0.127 
• R-Value Observed: 0.128 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.839	α = 90
b = 57.839	β = 90
c = 149.552	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Sugiyama, S., Shimizu, N., Maruyama, M., Sazaki, G., Hirose, M., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H.

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Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	23860028
JSPS KAKENHI	Japan	25650051
JSPS KAKENHI	Japan	25286051

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary