2HTN

E. coli bacterioferritin in its as-isolated form

• PDB DOI: https://doi.org/10.2210/pdb2HTN/pdb

• Classification: METAL BINDING PROTEIN, OXIDOREDUCTASE
• Organism(s): Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-07-26 Released: 2006-11-21 
• Deposition Author(s): van Eerde, A., Wolterink-Van Loo, S., Van Der Oost, J., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.188 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.

van Eerde, A., Wolterink-van Loo, S., van der Oost, J., Dijkstra, B.W.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1061-1066

• PubMed: 17077480 
• DOI: https://doi.org/10.1107/S1744309106039583
• Primary Citation of Related Structures:  
  2HTN


• PubMed Abstract: 
  

  Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 A resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on 'as-isolated' E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins.

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Organizational Affiliation: 

Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 151.5 kDa 
• Atom Count: 10,846 
• Modelled Residue Count: 1,264 
• Deposited Residue Count: 1,264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B, C, D, E, F, G, H	158	Escherichia coli BL21	Mutation(s): 0  EC: 1.16.3.1
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12)) Explore P0ABD3  Go to UniProtKB:  P0ABD3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	K [auth A], P [auth C], U [auth E], Z [auth G]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FE	AA [auth H], BA [auth H], I [auth A], J [auth A], L [auth B], M [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth E], T [auth E], V [auth F], W [auth F], X [auth G], Y [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.188 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.893	α = 90
b = 167.893	β = 90
c = 167.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): van Eerde, A., Wolterink-Van Loo, S., Van Der Oost, J., Dijkstra, B.W.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2014-11-12
  Changes: Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description