7R2O | pdb_00007r2o

Crystal structure of a flavodiiron protein S262Y mutant in the oxidized state from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb7R2O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-02-05 Released: 2023-02-15 
• Deposition Author(s): Borges, P.T., Teixeira, M., Romao, C.V., Frazao, C.
• Funding Organization(s): Foundation for Science and Technology (FCT)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: other

Literature

Crystal structure of a flavodiiron protein S262Y mutant in the oxidized state from Escherichia coli

Borges, P.T., Teixeira, M., Romao, C.V., Frazao, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110 kDa 
• Atom Count: 7,109 
• Modeled Residue Count: 802 
• Deposited Residue Count: 958 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaerobic nitric oxide reductase flavorubredoxin	A, B	479	Escherichia coli K-12	Mutation(s): 1  Gene Names: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680
UniProt
Find proteins for Q46877 (Escherichia coli (strain K12)) Explore Q46877  Go to UniProtKB:  Q46877

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FEO	D [auth A], G [auth B]	MU-OXO-DIIRON Fe2 O NPMYUMBHPJGBFA-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.968	α = 90
b = 64.019	β = 120.42
c = 88.882	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Borges, P.T., Teixeira, M., Romao, C.V., Frazao, C.

---

Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	United Kingdom	--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Refinement description