7TPN | pdb_00007tpn

Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN)

• PDB DOI: https://doi.org/10.2210/pdb7TPN/pdb

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


• Deposited: 2022-01-25 Released: 2022-09-14 
• Deposition Author(s): Buscagan, T.M., Kaiser, J.T., Rees, D.C.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Selenocyanate derived Se-incorporation into the Nitrogenase Fe protein cluster.

Buscagan, T.M., Kaiser, J.T., Rees, D.C.

(2022) Elife 11

• PubMed: 35904245 
• DOI: https://doi.org/10.7554/eLife.79311
• Primary Citation Related Structures: 
  7T4H, 7TNE, 7TPN, 7TPO, 7TPV, 7TPW, 7TPX, 7TPY, 7TPZ, 7TQ0, 7TQ9, 7TQC, 7TQE, 7TQF, 7TQH, 7TQI, 7TQJ, 7TQK


• PubMed Abstract: 
  

  The nitrogenase Fe protein mediates ATP-dependent electron transfer to the nitrogenase MoFe protein during nitrogen fixation, in addition to catalyzing MoFe protein-independent substrate (CO ₂ ) reduction and facilitating MoFe protein metallocluster biosynthesis. The precise role(s) of the Fe protein Fe ₄ S ₄ cluster in some of these processes remains ill-defined. Herein, we report crystallographic data demonstrating ATP-dependent chalcogenide exchange at the Fe ₄ S ₄ cluster of the nitrogenase Fe protein when potassium selenocyanate is used as the selenium source, an unexpected result as the Fe protein cluster is not traditionally perceived as a site of substrate binding within nitrogenase. The observed chalcogenide exchange illustrates that this Fe ₄ S ₄ cluster is capable of core substitution reactions under certain conditions, adding to the Fe protein's repertoire of unique properties.

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Organizational Affiliation: 
• Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.
Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.89 kDa 
• Atom Count: 2,367 
• Modeled Residue Count: 274 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron protein 1	A	290	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFS	C [auth A]	Fe4-Se4 cluster Fe4 Se4 HSQOKLBIIKAQNG-UHFFFAOYSA-N
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.996	α = 90
b = 74.633	β = 90
c = 75.137	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Buscagan, T.M., Kaiser, J.T., Rees, D.C.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description