1FXZ

CRYSTAL STRUCTURE OF SOYBEAN PROGLYCININ A1AB1B HOMOTRIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of soybean proglycinin A1aB1b homotrimer.

Adachi, M.Takenaka, Y.Gidamis, A.B.Mikami, B.Utsumi, S.

(2001) J Mol Biol 305: 291-305

  • DOI: https://doi.org/10.1006/jmbi.2000.4310
  • Primary Citation of Related Structures:  
    1FXZ

  • PubMed Abstract: 

    Soybean glycinin is a member of the 11 S globulin family. The crystal structure of proglycinin was determined by X-ray crystallography at 2.8 A resolution with an R-factor of 0.199 and a free R-factor of 0.250. A trimer molecule was found in an asymmetric unit of crystals. The trimer model contains three A1aB1b subunits and comprises 1128 amino acid residues and 34 water molecules. The constituent protomers of the homo-trimeric protein are arranged around a 3-fold symmetry axis with dimensions of 95 Ax95 Ax40 A. The protomer model is composed of five fragments which correspond roughly to conserved regions based on the sequence alignment of various 11 S globulins. The core of the protomer consists of two jelly-roll beta-barrels and two extended helix domains. This structure of proglycinin is similar to those of canavalin and phaseolin belonging to the 7 S globulin family, strongly supporting the hypothesis that both 7 S and 11 S globulins are derived from a common ancestor. The inter and intra-chain disulfide bonds conserved in the 11 S globulin family are clearly observed. It is found that the face with the inter-chain disulfide bond (IE face) contains more hydrophobic residues than that with the intra-chain disulfide bond. This suggests that a mature hexamer is formed by the interaction between the IE faces after processing.


  • Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji, Kyoto, 611-0011, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCININ G1
A, B, C
476Glycine maxMutation(s): 0 
UniProt
Find proteins for P04776 (Glycine max)
Explore P04776 
Go to UniProtKB:  P04776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04776
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.524α = 90
b = 115.524β = 90
c = 146.998γ = 90
Software Package:
Software NamePurpose
SADIEdata collection
SAINTdata reduction
PHASESphasing
X-PLORrefinement
SADIEdata reduction
SAINTdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance