1UIJ | pdb_00001uij

Crystal Structure Of Soybean beta-Conglycinin Beta Homotrimer (I122M/K124W)

• PDB DOI: https://doi.org/10.2210/pdb1UIJ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Glycine max
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-07-16 Released: 2004-07-16 
• Deposition Author(s): Maruyama, N., Maruyama, Y., Tsuruki, T., Okuda, E., Yoshikawa, M., Utsumi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.225 (DCC) 

Literature

Creation of soybean beta-conglycinin beta with strong phagocytosis-stimulating activity

Maruyama, N., Maruyama, Y., Tsuruki, T., Okuda, E., Yoshikawa, M., Utsumi, S.

(2003) Biochim Biophys Acta 1648: 99-104

• PubMed: 12758152 
• DOI: https://doi.org/10.1016/s1570-9639(03)00113-4
• Primary Citation Related Structures: 
  1UIJ


• PubMed Abstract: 
  

  beta-Conglycinin is composed of three kinds of subunit: alpha, alpha' and beta. A phagocytosis-stimulating peptide sequence (MITLAIPVNKPGR), soymetide, exists in the alpha' subunit of beta-conglycinin. Met at N terminus of the soymetide is essential for the activity. When Thr at the third residue from N terminus of the soymetide is replaced by Phe or Trp, the phagocytosis-stimulating activity greatly increases (ThrMet, Lys-->Thr, Phe, or Trp) into the beta subunit after confirmation of the effects of residue replacements by molecular modeling, suggesting that the introduced mutations might not prevent the correct folding. The studies of circular dichroism (CD), gel filtration and differential scanning calorimetry (DSC) of the mutants (I122M/K124T, I122M/K124F, I122M/K124W) expressed in E. coli demonstrated that they folded and self-assembled similarly to the wild type. This was confirmed by X-ray analysis of I122M/K124W crystal where the biggest residue tryptophane was introduced. The three mutants exhibited phagocytosis activities after digestion by trypsin, and the order was the wild type

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Organizational Affiliation: 
• Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 288.65 kDa 
• Atom Count: 18,133 
• Modeled Residue Count: 2,186 
• Deposited Residue Count: 2,496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta subunit of beta conglycinin	A, B, C, D, E, F	416	Glycine max	Mutation(s): 2
UniProt
Find proteins for P25974 (Glycine max) Explore P25974  Go to UniProtKB:  P25974

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.225 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.263	α = 90
b = 62.583	β = 90.44
c = 159.009	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-16 
Deposition Author(s): Maruyama, N., Maruyama, Y., Tsuruki, T., Okuda, E., Yoshikawa, M., Utsumi, S.

Revision History  

• Version 1.0: 2004-07-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references
• Version 1.4: 2023-12-27
  Changes: Data collection