9JN8 | pdb_00009jn8

Crystal structure of a thioredoxin-like ferredoxin of Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of a Thioredoxin-like Ferredoxin Encoded Within a Cobalamin Biosynthetic Operon of Rhodobacter capsulatus.

Shen, Y.H.Cheng, W.L.Wang, X.Dai, H.E.Wang, M.Liu, L.

(2025) Protein J 44: 192-200

  • DOI: https://doi.org/10.1007/s10930-025-10254-z
  • Primary Citation of Related Structures:  
    9JN8

  • PubMed Abstract: 

    Thioredoxin-like ferredoxin is a small homodimeric protein containing a [2Fe-2S] cluster in each monomer. It is only found in bacteria but its physiological function remains largely unknown. The cobalamin biosynthetic operon in the genome of the purple phototroph Rhodobacter capsulatus encodes a putative ferredoxin dubbed as CfrX. To characterize this protein, we cloned, expressed, purified, and crystalized the recombinant CfrX in the iron-sulfur cluster-bound state, and solved the structure at 2.1-Å resolution. Adopting a typical thioredoxin-like ferredoxin fold, a CfrX monomer binds one [2Fe-2S] cluster through four Cys residues located on two protruding loops. Unexpectedly, CfrX dimerizes in a previously unreported manner. With the structural information, we ascertained CfrX as a thioredoxin-like ferredoxin. While the precise function of CfrX in cobalamin biosynthesis is elusive, a link between CfrX and aerobic cobaltochelatase should exist due to the gene clustering pattern. We also discussed the possible relationship among CfrX, CobW, and CobNST with respect to the [2Fe-2S] cluster.


  • Organizational Affiliation
    • School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF378
A, B, C
133Rhodobacter capsulatusMutation(s): 0 
UniProt
Find proteins for D5AV11 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AV11 
Go to UniProtKB:  D5AV11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AV11
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.04α = 90
b = 60.04β = 90
c = 277.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32471323

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Database references