Biological Assembly 1  

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 453.53 kDa 
• Atom Count: 34,092 
• Modelled Residue Count: 3,712 
• Deposited Residue Count: 3,792 
• Unique protein chains: 1

 4TO9

2.0A resolution structure of BfrB (N148L) from Pseudomonas aeruginosa

• PDB DOI:  https://doi.org/10.2210/pdb4TO9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-06-05 Released: 2015-02-11 
• Deposition Author(s): Lovell, S., Battaile, K.P., Yao, H., Kumar, R., Eshelman, K., Rivera, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.

Yao, H., Rui, H., Kumar, R., Eshelman, K., Lovell, S., Battaile, K.P., Im, W., Rivera, M.

(2015) Biochemistry 54: 1611-1627

• PubMed: 25640193 
• DOI: https://doi.org/10.1021/bi501255r
• Primary Citation of Related Structures:  
  4TO9, 4TOA, 4TOB, 4TOC, 4TOD, 4TOE, 4TOF, 4TOG, 4TOH


• PubMed Abstract: 
  

X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.

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Organizational Affiliation: 

Department of Chemistry, ‡Del Shankel Structural Biology Center, and §Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	158	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: bfrB, PA3531 EC: 1.16.3.1
UniProt
Find proteins for Q9HY79 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HY79  Go to UniProtKB:  Q9HY79

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	AA [auth C], CA [auth F], DA [auth H], FA [auth J], GA [auth K], HA [auth N], IA [auth O], KA [auth Q], MA [auth S], OA [auth V], PA [auth W], Z [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
K	BA [auth E], EA [auth H], JA [auth O], LA [auth R], NA [auth S], Y [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.726	α = 90
b = 203.355	β = 90
c = 208.266	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Lovell, S., Battaile, K.P., Yao, H., Kumar, R., Eshelman, K., Rivera, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1158469

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence