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 6FEA | pdb_00006fea

A. vinelandii vanadium nitrogenase, turnover state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.145 (Depositor), 0.146 (DCC) 
  • R-Value Work: 
    0.117 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 
    0.118 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Literature

A bound reaction intermediate sheds light on the mechanism of nitrogenase.

Sippel, D., Rohde, M., Netzer, J., Trncik, C., Gies, J., Grunau, K., Djurdjevic, I., Decamps, L., Andrade, S.L.A., Einsle, O.

(2018) Science 359: 1484-1489

  • DOI: https://doi.org/10.1126/science.aar2765
  • Primary Citation Related Structures: 
    6FEA

  • PubMed Abstract: 

    Reduction of N 2 by nitrogenases occurs at an organometallic iron cofactor that commonly also contains either molybdenum or vanadium. The well-characterized resting state of the cofactor does not bind substrate, so its mode of action remains enigmatic. Carbon monoxide was recently found to replace a bridging sulfide, but the mechanistic relevance was unclear. Here we report the structural analysis of vanadium nitrogenase with a bound intermediate, interpreted as a μ 2 -bridging, protonated nitrogen that implies the site and mode of substrate binding to the cofactor. Binding results in a flip of amino acid glutamine 176, which hydrogen-bonds the ligand and creates a holding position for the displaced sulfide. The intermediate likely represents state E 6 or E 7 of the Thorneley-Lowe model and provides clues to the remainder of the catalytic cycle.


  • Organizational Affiliation: 
    • Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 243.92 kDa 
  • Atom Count: 19,493 
  • Modeled Residue Count: 2,074 
  • Deposited Residue Count: 2,124 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase protein alpha chain
A, D
474Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for C1DI25 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DI25 
Go to UniProtKB:  C1DI25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DI25
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vanadium nitrogenase beta subunit, vnfK
B, E
475Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for C1DI23 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DI23 
Go to UniProtKB:  C1DI23
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DI23
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vanadium nitrogenase, delta subunit, VnfG
C, F
113Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for C1DI24 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DI24 
Go to UniProtKB:  C1DI24
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DI24
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D6N

Query on D6N



Download:Ideal Coordinates CCD File
H [auth A],
Q [auth D]
FeV
C H Fe7 N S7 V
YNVNIECPQFRAMK-UHFFFAOYSA-N
CLF

Query on CLF



Download:Ideal Coordinates CCD File
L [auth A],
U [auth D]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA

Query on HCA



Download:Ideal Coordinates CCD File
G [auth A],
R [auth D]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A],
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3

Query on CO3



Download:Ideal Coordinates CCD File
I [auth A],
S [auth D]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
H2S

Query on H2S



Download:Ideal Coordinates CCD File
J [auth A],
T [auth D]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth B],
N [auth B],
P [auth C],
V [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.145 (Depositor), 0.146 (DCC) 
  • R-Value Work:  0.117 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 0.118 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.61α = 84.05
b = 79.75β = 72.44
c = 107.16γ = 75.25
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyRTG 1976
German Research FoundationGermanyPP 1927
European Research CouncilGermany310656

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2026-09-16
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary