6Q93

MgADP-bound Fe protein of Vanadium nitrogenase from Azotobacter vinelandii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Literature

Crystal structure of VnfH, the iron protein component of vanadium nitrogenase.

Rohde, M.Trncik, C.Sippel, D.Gerhardt, S.Einsle, O.

(2018) J Biol Inorg Chem 23: 1049-1056

  • DOI: https://doi.org/10.1007/s00775-018-1602-4
  • Primary Citation of Related Structures:  
    6Q93

  • PubMed Abstract: 

    Nitrogenases catalyze the biological fixation of inert N 2 into bioavailable ammonium. They are bipartite systems consisting of the catalytic dinitrogenase and a complementary reductase, the Fe protein that is also the site where ATP is hydrolyzed to drive the reaction forward. Three different subclasses of dinitrogenases are known, employing either molybdenum, vanadium or only iron at their active site cofactor. Although in all these classes the mode and mechanism of interaction with Fe protein is conserved, each one encodes its own orthologue of the reductase in the corresponding gene cluster. Here we present the 2.2 Å resolution structure of VnfH from Azotobacter vinelandii, the Fe protein of the alternative, vanadium-dependent nitrogenase system, in its ADP-bound state. VnfH adopts the same conformation that was observed for NifH, the Fe protein of molybdenum nitrogenase, in complex with ADP, representing a state of the functional cycle that is ready for reduction and subsequent nucleotide exchange. The overall similarity of NifH and VnfH confirms the experimentally determined cross-reactivity of both ATP-hydrolyzing reductases.


  • Organizational Affiliation

    Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein
A, B, C, D, E
A, B, C, D, E, F, G, H
290Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for C1DI30 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DI30 
Go to UniProtKB:  C1DI30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DI30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
J [auth A]
L [auth B]
O [auth C]
AA [auth G],
CA [auth H],
J [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
W [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C],
T [auth E],
Z [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
K [auth A]
M [auth B]
P [auth C]
BA [auth G],
DA [auth H],
K [auth A],
M [auth B],
P [auth C],
Q [auth C],
S [auth D],
V [auth E],
X [auth F],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.573α = 90
b = 176.857β = 90
c = 354.225γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany310656

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description