1FXZ

CRYSTAL STRUCTURE OF SOYBEAN PROGLYCININ A1AB1B HOMOTRIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 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: 10.1006/jmbi.2000.4310

  • 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 asymm ...

    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
    • An alternate cDNA encoding glycinin A1aBx subunit
      Utsumi, S.,Kohno, T.,Mori, T.,Kito, M.
      (1987) J.Agric.Food Chem. 35: 210
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCININ G1
A, B, C
476Glycine maxGene Names: GY1
Find proteins for P04776 (Glycine max)
Go to UniProtKB:  P04776
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 115.524α = 90.00
b = 115.524β = 90.00
c = 146.998γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
SADIEdata collection
SAINTdata reduction
SADIEdata reduction
X-PLORrefinement
SAINTdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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