2P0B | pdb_00002p0b

Crystal structure of chemically-reduced E.coli nrfB

• PDB DOI: https://doi.org/10.2210/pdb2P0B/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-28 Released: 2007-08-07 
• Deposition Author(s): Clarke, T.A., Richardson, D.J., Hemmings, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA.

Clarke, T.A., Cole, J.A., Richardson, D.J., Hemmings, A.M.

(2007) Biochem J 406: 19-30

• PubMed: 17521287 
• DOI: https://doi.org/10.1042/BJ20070321
• Primary Citation Related Structures: 
  2OZY, 2P0B


• PubMed Abstract: 
  

  NrfB is a small pentahaem electron-transfer protein widely involved in the respiratory reduction of nitrite or nitric oxide to ammonia, processes that provide energy for anaerobic metabolism in many enteric bacteria and also serve to detoxify these reactive nitrogen species. The X-ray crystal structure of Escherichia coli NrfB is presented at 1.74 A (1 A=0.1 nm) resolution. The architecture of the protein is that of a 40 A 'nanowire' in which the five haems are positioned within 6 A of each other along a polypeptide scaffold. During nitrite reduction, the physiological role of NrfB is to mediate electron transfer to another pentahaem protein, NrfA, the enzyme that catalyses periplasmic nitrite or nitric oxide reduction. Protein-protein interaction studies suggest NrfA and NrfB can form a 20-haem NrfA2-NrfB2 heterotetrameric complex.

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Organizational Affiliation: 
• Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.28 kDa 
• Atom Count: 1,595 
• Modeled Residue Count: 142 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-type protein nrfB	A	163	Escherichia coli K-12	Mutation(s): 0  Gene Names: nrfB
UniProt
Find proteins for P0ABL1 (Escherichia coli (strain K12)) Explore P0ABL1  Go to UniProtKB:  P0ABL1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.727	α = 90
b = 59.433	β = 90
c = 65.318	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Clarke, T.A., Richardson, D.J., Hemmings, A.M.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary