8BOQ | pdb_00008boq

A. vinelandii Fe-nitrogenase FeFe protein

• PDB DOI: https://doi.org/10.2210/pdb8BOQ/pdb

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


• Deposited: 2022-11-15 Released: 2023-06-14 
• Deposition Author(s): Trncik, C., Detemple, F., 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: 1.55 Å
• R-Value Free: 
  0.215 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Iron-only Fe-nitrogenase underscores common catalytic principles in biological nitrogen fixation

Trncik, C., Detemple, F., Einsle, O.

(2023) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-023-00952-1

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 250.18 kDa 
• Atom Count: 18,904 
• Modeled Residue Count: 2,188 
• Deposited Residue Count: 2,190 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	A, D	515	Azotobacter vinelandii DJ	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P16266 (Azotobacter vinelandii) Explore P16266  Go to UniProtKB:  P16266

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-only nitrogenase, beta subunit	B, E	461	Azotobacter vinelandii DJ	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P16267 (Azotobacter vinelandii) Explore P16267  Go to UniProtKB:  P16267

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron-iron protein delta chain	C, F	119	Azotobacter vinelandii DJ	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P16268 (Azotobacter vinelandii) Explore P16268  Go to UniProtKB:  P16268

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S5Q (Subject of Investigation/LOI)	G [auth A], N [auth D]	FeFe cofactor C Fe8 S9 ARHQIUGQOSHZFD-UHFFFAOYSA-N
CLF	I [auth A], R [auth E]	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA	H [auth A], O [auth D]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C7 H10 O7 XKJVEVRQMLKSMO-SSDOTTSWSA-N
H2S	K [auth A], Q [auth D]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N
MG	L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
O	J [auth A], P [auth D]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.215 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.969	α = 90
b = 151.048	β = 90
c = 158.863	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Trncik, C., Detemple, F., Einsle, O.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	PP 1927, project ID 311061829
German Research Foundation (DFG)	Germany	RTG 1976, project ID 235777276
European Research Council (ERC)	European Union	310676

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection