1UIK

Crystal structure of soybean beta-conglycinin alpha prime homotrimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the core region of the soybean beta-conglycinin alpha' subunit.

Maruyama, Y.Maruyama, N.Mikami, B.Utsumi, S.

(2004) Acta Crystallogr.,Sect.D 60: 289-297

  • DOI: 10.1107/S0907444903027367

  • PubMed Abstract: 
  • The crystal structure of the core region of the alpha' subunit (alpha(c')) of soybean beta-conglycinin has been determined at 2.3 A resolution. alpha(c') was superimposed on the known crystal structure of the beta-conglycinin beta subunit with a smal ...

    The crystal structure of the core region of the alpha' subunit (alpha(c')) of soybean beta-conglycinin has been determined at 2.3 A resolution. alpha(c') was superimposed on the known crystal structure of the beta-conglycinin beta subunit with a small root-mean square deviation of 0.77 A, which is consistent with the high sequence identity of 75.5% between alpha(c') and the beta subunit. It is known that the thermal stability of the beta subunit is higher than that of the alpha' subunit and that their thermal stabilities are conferred by highly homologous core regions. Comparisons of the three-dimensional structures and primary sequences between alpha(c') and the beta subunit suggest that five factors account for this difference between subunits as regards the difference in thermal stability: (i) the total cavity volume is larger in alpha(c'), (ii) the cluster of charged residues at the intermonomer interface is smaller in alpha(c') and alpha(c') lacks the intermonomer salt bridge of the beta subunit, (iii) the solvent-accessible surface is more hydrophobic in alpha(c'), (iv) there are fewer proline residues in alpha(c') and (v) a loop region between helix 3 and strand J' in alpha(c') is more flexible owing to the insertion of five additional residues. Although more hydrogen bonds were found in alpha(c'), this difference should be more than compensated for by the combined contributions of these other factors.


    Organizational Affiliation

    Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha prime subunit of beta-conglycinin
A, B, C
418Glycine maxMutation(s): 0 
Find proteins for Q7XXT2 (Glycine max)
Go to UniProtKB:  Q7XXT2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 164.960α = 90.00
b = 164.960β = 90.00
c = 110.050γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model