4AM5

Bacterioferritin from Blastochloris viridis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIOFERRITINA, B159Blastochloris viridisMutation(s): 0 
Gene Names: bfrBV133_1877BVIRIDIS_22540
EC: 1.16.3.1
Find proteins for K7N5M0 (Blastochloris viridis)
Explore K7N5M0 
Go to UniProtKB:  K7N5M0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth B], G [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.156 
  • 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

View Full Validation Report



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: 2015-02-04
    Changes: Atomic model, Derived calculations, Other
  • Version 1.3: 2017-12-13
    Changes: Database references, Structure summary
  • Version 1.4: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation