Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 144.56 kDa 
• Atom Count: 8881 
• Modelled Residue Count: 1088 
• Deposited Residue Count: 1248 
• Unique protein chains: 1

1IPJ

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

• PDB DOI: 10.2210/pdb1IPJ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Glycine max
• Mutation(s): No 


• Deposited: 2001-05-16 Released: 2002-05-16 
• Deposition Author(s): Maruyama, N., Adachi, M., Takahashi, K., Yagasaki, K., Kohno, M., Takenaka, Y., Okuda, E., Nakagawa, S., Mikami, B., Utsumi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.284 
• R-Value Work: 0.202 

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

• PubMed: 11422391 
• DOI: 10.1046/j.1432-1327.2001.02268.x
• Primary Citation of Related Structures:  
  1IPJ, 1IPK


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-CONGLYCININ, BETA CHAIN	A, B, C	416	Glycine max	Mutation(s): 0  Gene Names: CG-4, GLYMA_20G146200
UniProt
Find proteins for P25974 (Glycine max) Explore P25974  Go to UniProtKB:  P25974

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth B], F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.284 
• R-Value Work: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.78	α = 90
b = 69.47	β = 97.22
c = 125.33	γ = 90

Software Package:

Software Name	Purpose
FRAMBO	data collection
SAINT	data reduction
X-PLOR	model building
X-PLOR	refinement
SAINT	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-16 
• Released Date: 2002-05-16 
Deposition Author(s): Maruyama, N., Adachi, M., Takahashi, K., Yagasaki, K., Kohno, M., Takenaka, Y., Okuda, E., Nakagawa, S., Mikami, B., Utsumi, S.

Revision History  

• Version 1.0: 2002-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary