8SQQ | pdb_00008sqq

Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (Apo Cubic Form 2, F16L mutant)

• PDB DOI: https://doi.org/10.2210/pdb8SQQ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-05-04 Released: 2023-05-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural Analysis and Inhibitor Modeling of Bacterioferritin From Brucella abortus.

Liu, L., Harmon, E.K., Craig, J.K., Yao, H., Battaile, K.P., Johnson, D.K., Subramanian, S., Van Voorhis, W.C., Rivera, M., Lovell, S.

(2026) Proteins 

• PubMed: 41482512 
• DOI: https://doi.org/10.1002/prot.70109
• Primary Citation of Related Structures:  
  8SQO, 8SQP, 8SQQ, 8SQR, 8SQT


• PubMed Abstract: 
  

  Iron homeostasis in various pathogenic bacteria is regulated by bacterioferritins (Bfr) which function to store Fe ³⁺ and release Fe ²⁺ as needed for metabolic processes. The Bfr structure consists of 18 kDa subunits in which dimer pairs bind a heme molecule and are assembled into a highly symmetrical 24-meric spherical structure with an internal core diameter of approximately 80 Å. Release of iron is facilitated by the binding of a 7 kDa [2Fe-2S] ferredoxin (Bfd) to specific sites on the surface of Bfr which transfers electrons to the core thereby reducing the stored Fe ³⁺ to Fe ²⁺ for mobilization. The crystal structures of Bfr from Brucella abortus (Ba) in the apo and iron bound forms are presented and compared with those from Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa). Additionally, models of the Bfr:Bfd complexes for Ba and Ab are provided and compared with the Pa complex. Finally, compounds known to target the Bfr:Bfd interaction in Pa were docked to the Ba and Ab structures which provided insight regarding the potential binding mode and inhibitory mechanism.

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Organizational Affiliation: 
• Protein Structure and X-Ray Crystallography Laboratory, Del Shankel Structural Biology Center, University of Kansas, Kansas, USA.
Seattle Structural Genomics Center for Infectious Diseases, Washington, USA.
Center for Emerging and re-Emerging Infectious Diseases (CERID), division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Washington, USA.
Department of Chemistry, Louisiana State University, Louisiana, USA.
New York Structural Biology Center, New York, New York, USA.
Molecular Graphics and Modeling Laboratory and the Computational Chemical Biology Core, University of Kansas, Kansas, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.74 kDa 
• Atom Count: 1,378 
• Modeled Residue Count: 160 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A	165	Brucella abortus 2308	Mutation(s): 1  Gene Names: bfr, BAB2_0675 EC: 1.16.3.1
UniProt
Find proteins for Q2YKI4 (Brucella abortus (strain 2308)) Explore Q2YKI4  Go to UniProtKB:  Q2YKI4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38SQQ

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.516	α = 90
b = 171.516	β = 90
c = 171.516	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection
• Version 1.2: 2026-01-14
  Changes: Database references, Structure summary