Ferredoxin VI from Rhodobacter Capsulatus

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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This is version 1.4 of the entry. See complete history


Crystallization and Preliminary X-Ray Diffraction Analysis of a [2Fe-2S] Ferredoxin (Fdvi) from Rhodobacter Capsulatus

Armengaud, J.Sainz, G.Jouanneau, Y.Sieker, L.C.

(2001) Acta Crystallogr D Biol Crystallogr 57: 301

  • DOI: https://doi.org/10.1107/s0907444900017832
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A [2Fe-2S] ferredoxin found in the photosynthetic bacterium Rhodobacter capsulatus has been purified in recombinant form from Escherichia coli. This protein, called FdVI, resembles ferredoxins involved in iron-sulfur cluster biosynthesis in various prokaryotic and eukaryotic cells. Purified recombinant FdVI was recovered in high yields and appeared to be indistinguishable from the genuine R. capsulatus ferredoxin based on UV-visible absorption and EPR spectroscopy and mass spectrometry. FdVI has been crystallized in the oxidized state by a sitting-drop vapour-diffusion technique using sodium formate as precipitant. Seeding larger drops from a previous hanging-drop-grown small crystal resulted in the formation of long red-brown prismatic needles. Preliminary X-ray diffraction analysis indicated that FdVI crystals are orthorhombic and belong to the space group P2(1)2(1)2(1), with unit-cell parameters a = 45.87, b = 49.83, c = 54.29 A.

  • Organizational Affiliation

    Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, CNRS UMR 5092, Département de Biologie Moléculaire et Structurale, CEA-Grenoble, F-38054 Grenoble CEDEX 9, France.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERREDOXIN VI106Rhodobacter capsulatusMutation(s): 0 
Gene Names: FDXE
Find proteins for P80306 (Rhodobacter capsulatus)
Explore P80306 
Go to UniProtKB:  P80306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80306
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FES

Download Ideal Coordinates CCD File 
Fe2 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.34α = 90
b = 49.03β = 90
c = 54.91γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations