9I2A | pdb_00009i2a

FdC of Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9I2A

This is version 1.1 of the entry. See complete history

Literature

Two Key Ferredoxins for Nitrogen Fixation Have Different Specificities and Biophysical Properties.

Addison, H.Pfister, P.Lago-Maciel, A.Erb, T.J.Pierik, A.J.Rebelein, J.G.

(2025) Chemistry 31: e202500844-e202500844

  • DOI: https://doi.org/10.1002/chem.202500844
  • Primary Citation Related Structures: 
    9I2A

  • PubMed Abstract: 

    Ferredoxins deliver electrons to drive many challenging biochemical transformations, including enzyme-catalyzed nitrogen fixation. We recently showed two distinct ferredoxins, FdC and FdN, were essential for iron nitrogenase-mediated nitrogen fixation in R. capsulatus. In this study, we perform investigations on FdC and FdN to establish their key differences in terms of specificity, structure, and electronic properties. In vivo complementation studies of both the genes encoding FdC (fdxC) and FdN (fdxN), into ∆fdxC and ∆fdxN R. capsulatus-deletion strains under N 2 -fixing conditions, showed that plasmid-based expression of fdxN recovered diazotrophic growth and Fe-nitrogenase activity in both ∆fdxC and ∆fdxN strains, while plasmid-based fdxC expression could only complement the ∆fdxC strain. Spectroscopic analysis of FdC and FdN using electron paramagnetic resonance spectroscopy revealed large differences in the electronic features of FdC and FdN. These differences were accompanied by large structural differences between FdC and FdN, assessed by a crystallographic structure of FdC and an AlphaFold model of FdN. We report novel features in the FdC structure, in terms of secondary structure and hydrogen-bonding network, compared with structures of other [Fe 2 S 2 ]-cluster ferredoxins. Overall, we explore the biophysical properties that influence ferredoxin specificity, while providing new insights into the properties of ferredoxins essential for N 2 -fixation.


  • Organizational Affiliation
    • Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany.

Macromolecule Content 

  • Total Structure Weight: 22.93 kDa 
  • Atom Count: 1,526 
  • Modeled Residue Count: 191 
  • Deposited Residue Count: 208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-4
A, B
104Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ARY7 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5ARY7 
Go to UniProtKB:  D5ARY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ARY7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.87α = 90
b = 45.83β = 90
c = 85.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references