7N2X

The crystal structure of an FMN-dependent NADH:quinone oxidoreductase, AzoR from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb7N2X/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-30 Released: 2022-08-31 
• Deposition Author(s): Arcinas, A.J., Fedorov, E., Kelly, L., Almo, S.C., Ghosh, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.190 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Uncovering a novel mechanism of enzyme activation in multimeric azoreductases

Hitchings, R., Ryan, A., Arcinas, A.J., Ghosh, A., Almo, S.C., Kelly, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.12 kDa 
• Atom Count: 1,781 
• Modelled Residue Count: 201 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent NADH:quinone oxidoreductase	A	223	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: azoR, Z2315, ECs2014 EC: 1.6.5 (PDB Primary Data), 1.7.1.17 (PDB Primary Data)
UniProt
Find proteins for P41407 (Escherichia coli (strain K12)) Explore P41407  Go to UniProtKB:  P41407

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
P4G	E [auth A]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N
DHA	D [auth A]	2-AMINO-ACRYLIC ACID C3 H5 N O2 UQBOJOOOTLPNST-UHFFFAOYSA-N
EDO	C [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.190 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.355	α = 90
b = 94.355	β = 90
c = 53.081	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Arcinas, A.J., Fedorov, E., Kelly, L., Almo, S.C., Ghosh, A.

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description