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 

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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: 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 ...

    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.


    Related Citations: 
    • Crystallization and preliminary X-ray Crystallographic analysis of the soybean proglycinin expressed in Escherichia coli.
      Utsumi, S., Gidamis, A.B., Mikami, B., Kito, M.
      (1993) J Mol Biol 233: 177
    • Signal sequence of preproglycinin affects production of the expressed protein in Escherichia coli.
      Utsumi, S., Kim, C.S., Sato, T., Kito, M.
      (1988) Gene 71: 349
    • An alternate cDNA encoding glycinin A1aBx subunit
      Utsumi, S., Kohno, T., Mori, T., Kito, M.
      (1987) J Agric Food Chem 35: 210

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCININ G1A, B, C476Glycine maxMutation(s): 0 
Gene Names: GY1Glyma03g32030
UniProt
Find proteins for P04776 (Glycine max)
Explore P04776 
Go to UniProtKB:  P04776
Protein Feature View
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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

View Full Validation Report




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