4AM2

Bacterioferritin from Blastochloris viridis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural Characterization of Bacterioferritin from Blastochloris Viridis.

Wahlgren, W.Y.Omran, H.von Stetten, D.Royant, A.van der Post, S.Katona, G.

(2012) PLoS One 7: 46992

  • DOI: https://doi.org/10.1371/journal.pone.0046992
  • Primary Citation of Related Structures:  
    4AM2, 4AM4, 4AM5

  • PubMed Abstract: 

    Iron storage and elimination of toxic ferrous iron are the responsibility of bacterioferritins in bacterial species. Bacterioferritins are capable of oxidizing iron using molecular oxygen and import iron ions into the large central cavity of the protein, where they are stored in a mineralized form. We isolated, crystallized bacterioferritin from the microaerophilic/anaerobic, purple non-sulfur bacterium Blastochloris viridis and determined its amino acid sequence and X-ray structure. The structure and sequence revealed similarity to other purple bacterial species with substantial differences in the pore regions. Static 3- and 4-fold pores do not allow the passage of iron ions even though structural dynamics may assist the iron gating. On the other hand the B-pore is open to water and larger ions in its native state. In order to study the mechanism of iron import, multiple soaking experiments were performed. Upon Fe(II) and urea treatment the ferroxidase site undergoes reorganization as seen in bacterioferritin from Escherichia coli and Pseudomonas aeruginosa. When soaking with Fe(II) only, a closely bound small molecular ligand is observed close to Fe(1) and the coordination of Glu94 to Fe(2) changes from bidentate to monodentate. DFT calculations indicate that the bound ligand is most likely a water or a hydroxide molecule representing a product complex. On the other hand the different soaking treatments did not modify the conformation of other pore regions.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BACTERIOFERRITIN
A, B
159Blastochloris viridisMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for K7N5M0 (Blastochloris viridis)
Explore K7N5M0 
Go to UniProtKB:  K7N5M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7N5M0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.2α = 90
b = 170.2β = 90
c = 170.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references, Structure summary
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description