6N4K

Dithionite-reduced nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii

• PDB DOI: https://doi.org/10.2210/pdb6N4K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2018-11-19 Released: 2019-02-13 
• Deposition Author(s): Wenke, B.B., Spatzal, T., Rees, D.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.213 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0States of the Nitrogenase Fe-Protein.

Wenke, B.B., Spatzal, T., Rees, D.C.

(2019) Angew Chem Int Ed Engl 58: 3894-3897

• PubMed: 30698901 
• DOI: https://doi.org/10.1002/anie.201813966
• Primary Citation of Related Structures:  
  6N4J, 6N4K, 6N4L, 6N4M


• PubMed Abstract: 
  

  The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+, and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-Å resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S] ¹⁺ state, our analysis identifies a solvent exposed, delocalized Fe ^2.5+ pair and a buried Fe ²⁺ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S] ⁰ and [4Fe:4S] ²⁺ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe ²⁺ and valence delocalized Fe ^2.5+ , respectively.

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Organizational Affiliation: 

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 63.19 kDa 
• Atom Count: 4,147 
• Modelled Residue Count: 542 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron protein 1	A, B	289	Azotobacter vinelandii	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii) Explore P00459  Go to UniProtKB:  P00459

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.213 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.62	α = 90
b = 45.199	β = 96.58
c = 108.772	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-13 
Deposition Author(s): Wenke, B.B., Spatzal, T., Rees, D.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM045162

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description