1IPJ

CRYSTAL STRUCTURES OF RECOMBINANT AND NATIVE SOYBEAN BETA-CONGLYCININ BETA HOMOTRIMERS COMPLEXES WITH N-ACETYL-D-GLUCOSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers.

Maruyama, N.Adachi, M.Takahashi, K.Yagasaki, K.Kohno, M.Takenaka, Y.Okuda, E.Nakagawa, S.Mikami, B.Utsumi, S.

(2001) Eur.J.Biochem. 268: 3595-3604

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of recombinant and native beta homotrimers of soybean beta-conglycinin were determined by X-ray crystallography at 2.7 and 2.8 A resolutions, respectively. The crystals of the recombinant and native beta homotrimers belong to s ...

    The crystal structures of recombinant and native beta homotrimers of soybean beta-conglycinin were determined by X-ray crystallography at 2.7 and 2.8 A resolutions, respectively. The crystals of the recombinant and native beta homotrimers belong to space group P21 with cell parameters a = 80.51 A, b = 63.48 A, c = 131.43 A, and beta = 90.01 degrees and with cell parameters a = 82.78 A, b = 69.47 A, c = 125.33 A and beta = 97.22 degrees, respectively. The beta monomers consist of amino-terminal and carboxyl-terminal modules that are very similar to each other and are related by a pseudo-dyad axis. Each module of the beta monomer is subdivided into a core and a loop domain. These structural features of both beta homotrimers are consistent with those of canavalin and phaseolin, which are similar vicilin class proteins. The superposition of the models of the native and recombinant beta monomers shows a root mean square deviation of 0.43-0.51 A for 343 common Calpha atoms within 2.0 A. This result indicates that the N-linked glycans do not influence the final structure of the beta homotrimer. Comparison of the models of beta-conglycinin, phaseolin and canavalin indicates that beta-conglycinin resembles canavalin rather than phaseolin, and that canavalin and phaseolin differ the most among them. The evolutional relationships are discussed.


    Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-CONGLYCININ, BETA CHAIN
A, B, C
416Glycine maxMutation(s): 0 
Gene Names: CG-4
Find proteins for P25974 (Glycine max)
Go to UniProtKB:  P25974
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.780α = 90.00
b = 69.470β = 97.22
c = 125.330γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
FRAMBOdata collection
X-PLORmodel building
X-PLORrefinement
SAINTdata scaling
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description