7AIZ | pdb_00007aiz

Vanadium nitrogenase VFe protein, high CO state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.146 (Depositor), 0.146 (DCC) 
  • R-Value Work: 
    0.124 (Depositor) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle.

Rohde, M.Laun, K.Zebger, I.Stripp, S.T.Einsle, O.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abg4474
  • Primary Citation Related Structures: 
    7AIZ

  • PubMed Abstract: 

    Besides its role in biological nitrogen fixation, vanadium-containing nitrogenase also reduces carbon monoxide (CO) to hydrocarbons, in analogy to the industrial Fischer-Tropsch process. The protein yields 93% of ethylene (C 2 H 4 ), implying a C-C coupling step that mandates the simultaneous binding of two CO at the active site FeV cofactor. Spectroscopic data indicated multiple CO binding events, but structural analyses of Mo and V nitrogenase only confirmed a single site. Here, we report the structure of a two CO-bound state of V nitrogenase at 1.05 Å resolution, with one μ-bridging and one terminal CO molecule. This additional, specific ligand binding site suggests a mechanistic route for CO reduction and hydrocarbon formation, as well as a second access pathway for protons required during the reaction. Moreover, carbonyls are strong-field ligands that are chemically similar to mechanistically relevant hydrides that may be formed and used in a fully analogous fashion.


  • Organizational Affiliation
    • Institute for Biochemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 244.88 kDa 
  • Atom Count: 19,918 
  • Modeled Residue Count: 2,098 
  • Deposited Residue Count: 2,124 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase vanadium-iron protein alpha chain
A, D
474Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfD
EC: 1.18.6.1
UniProt
Find proteins for P16855 (Azotobacter vinelandii)
Explore P16855 
Go to UniProtKB:  P16855
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16855
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase vanadium-iron protein beta chain
B, E
475Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfK
EC: 1.18.6.1
UniProt
Find proteins for P16856 (Azotobacter vinelandii)
Explore P16856 
Go to UniProtKB:  P16856
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16856
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase vanadium-iron protein delta chain
C, F
113Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfG
EC: 1.18.6.1
UniProt
Find proteins for P16857 (Azotobacter vinelandii)
Explore P16857 
Go to UniProtKB:  P16857
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16857
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D6N
(Subject of Investigation/LOI)

Query on D6N



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

Query on CLF



Download:Ideal Coordinates CCD File
DA [auth E],
P [auth B]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA

Query on HCA



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

Query on TRS



Download:Ideal Coordinates CCD File
CA [auth D],
N [auth A],
O [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO

Query on EDO



Download:Ideal Coordinates CCD File
EA [auth E]
FA [auth E]
GA [auth E]
HA [auth E]
JA [auth F]
EA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
JA [auth F],
L [auth A],
M [auth A],
S [auth B],
T [auth B],
U [auth B],
W [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
I [auth A],
Z [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CMO
(Subject of Investigation/LOI)

Query on CMO



Download:Ideal Coordinates CCD File
AA [auth D],
BA [auth D],
J [auth A],
K [auth A]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free:  0.146 (Depositor), 0.146 (DCC) 
  • R-Value Work:  0.124 (Depositor) 
  • R-Value Observed: 0.126 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.521α = 84
b = 80.041β = 72.48
c = 107.21γ = 75.03
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany310656
German Research Foundation (DFG)GermanyRTG 1976, project no. 235777276
German Research Foundation (DFG)GermanyPP 1927, project no. 311061829

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description