3U7Q

A. vinelandii nitrogenase MoFe protein at atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb3U7Q/pdb

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


• Deposited: 2011-10-14 Released: 2011-12-07 
• Deposition Author(s): Spatzal, T., Einsle, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.146 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 

Starting Model: experimental

Literature

Evidence for interstitial carbon in nitrogenase FeMo cofactor.

Spatzal, T., Aksoyoglu, M., Zhang, L., Andrade, S.L., Schleicher, E., Weber, S., Rees, D.C., Einsle, O.

(2011) Science 334: 940-940

• PubMed: 22096190 
• DOI: https://doi.org/10.1126/science.1214025
• Primary Citation of Related Structures:  
  3U7Q


• PubMed Abstract: 
  

  The identity of the interstitial light atom in the center of the FeMo cofactor of nitrogenase has been enigmatic since its discovery. Atomic-resolution x-ray diffraction data and an electron spin echo envelope modulation (ESEEM) analysis now provide direct evidence that the ligand is a carbon species.

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Organizational Affiliation: 

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 235.15 kDa 
• Atom Count: 18,955 
• Modelled Residue Count: 1,998 
• Deposited Residue Count: 2,030 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	492	Azotobacter vinelandii	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii) Explore P07328  Go to UniProtKB:  P07328

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	523	Azotobacter vinelandii	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii) Explore P07329  Go to UniProtKB:  P07329

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ICS	F [auth A], Q [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe7 Mo S9 DDQFAOMIVKLFON-UHFFFAOYSA-N
1CL	J [auth B], T [auth D]	FE(8)-S(7) CLUSTER, OXIDIZED Fe8 S7 JKVMXLBGZBULKV-UHFFFAOYSA-N
CLF	K [auth B], V [auth D]	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA	E [auth A], P [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C7 H10 O7 XKJVEVRQMLKSMO-SSDOTTSWSA-N
IMD	G [auth A], H [auth A], M [auth B], N [auth B], R [auth C], S [auth C], U [auth D], W [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	I [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	O [auth B], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.146 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.19	α = 90
b = 130.696	β = 110.67
c = 107.224	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Spatzal, T., Einsle, O.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description