5AVG

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1021/ja301584y
  • Primary Citation of Related Structures:  

  • 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 crystal ...

    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.


    Organizational Affiliation

    Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. sugiyama@chem.eng.osaka-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thaumatin-1
A
206Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
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 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.839α = 90.00
b = 57.839β = 90.00
c = 149.552γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan23860028
JSPS KAKENHIJapan25650051
JSPS KAKENHIJapan25286051

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release