6YAV

Structure of FeSII (Shethna) protein from Azotobacter vinelandii

• PDB DOI: https://doi.org/10.2210/pdb6YAV/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Azotobacter vinelandii
• Expression System: Escherichia coli KRX
• Mutation(s): No 


• Deposited: 2020-03-13 Released: 2021-03-31 
• Deposition Author(s): Kabasakal, B.V., Kung, W.K.A., Cotton, C.A.R., Lieber, L., McFarlane, C.R., Murray, J.W.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.225 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Structure of FeSII (Shethna) protein from Azotobacter vinelandii

Kabasakal, B.V., Kung, W.K.A., Cotton, C.A.R., Lieber, L., McFarlane, C.R., Murray, J.W.

To be published.

Biological Assembly 1  

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

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 Evidence: SAXS

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 67.53 kDa 
• Atom Count: 4,656 
• Modelled Residue Count: 585 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimeric (2Fe-2S) protein	A [auth E], B [auth A], C [auth B], D [auth C], E [auth D]	122	Azotobacter vinelandii	Mutation(s): 0
UniProt
Find proteins for Q44501 (Azotobacter vinelandii) Explore Q44501  Go to UniProtKB:  Q44501

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES (Subject of Investigation/LOI)	F [auth E], I [auth A], J [auth B], K [auth C], L [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL	G [auth E], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	H [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.225 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.24	α = 90
b = 135.1	β = 90
c = 37.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Kabasakal, B.V., Kung, W.K.A., Cotton, C.A.R., Lieber, L., McFarlane, C.R., Murray, J.W.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L011468/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/J014575/1

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description