7QQA

MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii

• PDB DOI: https://doi.org/10.2210/pdb7QQA/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2022-01-07 Released: 2022-06-22 
• Deposition Author(s): Trncik, C., Mueller, T., Franke, P., Einsle, O.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.249 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii

Trncik, C., Mueller, T., Franke, P., Einsle, O.

(2022) Journal Of Inorganic Biochemistry 227

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.

Macromolecule Content

• Total Structure Weight: 122.35 kDa 
• Atom Count: 9,212 
• Modelled Residue Count: 1,088 
• Deposited Residue Count: 1,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron protein	A, B, C, D	274	Azotobacter vinelandii	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for C1DK95 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DK95  Go to UniProtKB:  C1DK95

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], H [auth B], J [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)	G [auth A], L [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MG	F [auth A], I [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.249 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.677	α = 68.57
b = 80.366	β = 75.85
c = 80.024	γ = 76.03

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Trncik, C., Mueller, T., Franke, P., Einsle, O.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	European Union	235777276
German Research Foundation (DFG)	European Union	273919336
European Research Council (ERC)	European Union	310656

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description