2EA7

Crystal Structure of Adzuki Bean 7S Globulin-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization and crystallography of recombinant 7S globulins of Adzuki bean and structure-function relationships with 7S globulins of various crops.

Fukuda, T.Maruyama, N.Salleh, M.R.Mikami, B.Utsumi, S.

(2008) J.Agric.Food Chem. 56: 4145-4153

  • DOI: 10.1021/jf072667b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recombinant proteins Adzuki 7S1, Adzuki 7S2, and Adzuki 7S3 were prepared through the Escherichia coli expression systems of three kinds of adzuki bean cDNAs. The recombinant proteins exhibited intrinsic thermal stabilities, surface hydrophobicit ...

    The recombinant proteins Adzuki 7S1, Adzuki 7S2, and Adzuki 7S3 were prepared through the Escherichia coli expression systems of three kinds of adzuki bean cDNAs. The recombinant proteins exhibited intrinsic thermal stabilities, surface hydrophobicities, and solubilities, although the homology of their amino acid sequences ranged from 95-98%. To understand why these individual proteins exhibited different properties, their three-dimensional structures were elucidated. The three proteins were successfully crystallized, and the three-dimensional structures of Adzuki 7S1 and Adzuki 7S3 were determined. The properties and structures of these two proteins were comprehensively compared with those of recombinant 7S globulins (soybean beta-conglycinins beta and alpha'c and mungbean 8Salpha) reported previously. It was likely that cavity sizes, hydrogen bonds, salt bridges, hydrophobic interactions, and lengths of loops determine the thermal stabilities of 7S globulins, and results indicated that cavity sizes strongly contribute to such stability. Surface hydrophobicity was also found to be determined not only by distributions of hydrophobic residues on the molecular surface. Furthermore, solubility at neutral and weak alkaline pH values at mu = 0.08 was found to be dominantly influenced by the electrostatic surface potentials.


    Organizational Affiliation

    Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7S globulin-1
A, B, C
434Phaseolus angularisMutation(s): 0 
Gene Names: 7S-1
Find proteins for A4PI98 (Phaseolus angularis)
Go to UniProtKB:  A4PI98
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B, C
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 101.598α = 90.00
b = 48.550β = 97.12
c = 119.765γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data scaling
HKL-2000data collection
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance