4GGR

The structure of apo bradavidin2 (Form A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins.

Leppiniemi, J.Meir, A.Kahkonen, N.Kukkurainen, S.Maatta, J.A.Ojanen, M.Janis, J.Kulomaa, M.S.Livnah, O.Hytonen, V.P.

(2013) Protein Sci. 22: 980-994

  • DOI: 10.1002/pro.2281
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bradavidin II is a biotin-binding protein from Bradyrhizobium japonicum that resembles chicken avidin and bacterial streptavidin. A biophysical characterization was carried out using dynamic light scattering, native mass spectrometry, differential sc ...

    Bradavidin II is a biotin-binding protein from Bradyrhizobium japonicum that resembles chicken avidin and bacterial streptavidin. A biophysical characterization was carried out using dynamic light scattering, native mass spectrometry, differential scanning calorimetry, and isothermal titration calorimetry combined with structural characterization using X-ray crystallography. These observations revealed that bradavidin II differs from canonical homotetrameric avidin protein family members in its quaternary structure. In contrast with the other avidins, bradavidin II appears to have a dynamic (transient) oligomeric state in solution. It is monomeric at low protein concentrations but forms higher oligomeric assemblies at higher concentrations. The crystal structure of bradavidin II revealed an important role for Phe42 in shielding the bound ligand from surrounding water molecules, thus functionally replacing the L7,8 loop essential for tight ligand binding in avidin and streptavidin. This bradavidin II characterization opens new avenues for oligomerization-independent biotin-binding protein development.


    Organizational Affiliation

    Institute of Biomedical Technology, University of Tampere and Tampere University Hospital, FI-33014, Tampere, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bradavidin 2
A
115Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)Mutation(s): 0 
Find proteins for Q89U61 (Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110))
Go to UniProtKB:  Q89U61
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 62.099α = 90.00
b = 46.061β = 116.66
c = 47.180γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-07 
  • Released Date: 2013-06-19 
  • Deposition Author(s): Livnah, O., Meir, A.

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references