1JM1

Crystal structure of the soluble domain of the Rieske protein II (soxF) from Sulfolobus acidocaldarius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.106 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution.

Bonisch, H.Schmidt, C.L.Schafer, G.Ladenstein, R.

(2002) J Mol Biol 319: 791-805

  • DOI: 10.1016/S0022-2836(02)00323-6
  • Primary Citation of Related Structures:  
    1JM1

  • PubMed Abstract: 
  • The first crystal structure of an archaeal Rieske iron-sulfur protein, the soluble domain of Rieske iron-sulfur protein II (soxF) from the hyperthermo-acidophile Sulfolobus acidocaldarius, has been solved by multiple wavelength anomalous dispersion (MAD) and has been refined to 1 ...

    The first crystal structure of an archaeal Rieske iron-sulfur protein, the soluble domain of Rieske iron-sulfur protein II (soxF) from the hyperthermo-acidophile Sulfolobus acidocaldarius, has been solved by multiple wavelength anomalous dispersion (MAD) and has been refined to 1.1 A resolution. SoxF is a subunit of the terminal oxidase supercomplex SoxM in the plasma membrane of S. acidocaldarius that combines features of a cytochrome bc(1) complex and a cytochrome c oxidase. The [2Fe-2S] cluster of soxF is most likely the primary electron acceptor during the oxidation of caldariella quinone by the cytochrome a(587)/Rieske subcomplex. The geometry of the [2Fe-2S] cluster and the structure of the cluster-binding site are almost identical in soxF and the Rieske proteins from eucaryal cytochrome bc(1) and b(6)f complexes, suggesting a strict conservation of the catalytic mechanism. The main domain of soxF and part of the cluster-binding domain, though structurally related, show a significantly divergent structure with respect to topology, non-covalent interactions and surface charges. The divergent structure of soxF reflects a different topology of the soxM complex compared to eucaryal bc complexes and the adaptation of the protein to the extreme ambient conditions on the outer membrane surface of a hyperthermo-acidophilic organism.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of Rieske iron-sulfur protein II (soxF) from Sulfolobus acidocaldarius
      Boenisch, H., Schmidt, C.L., Schaefer, G., Ladenstein, R.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 643
    • Expression of the Sulfolobus acidocaldarius Rieske iron sulfur protein II (soxF) with the correctly inserted [2Fe-2S] cluster in Escherichia coli
      Schmidt, C.L., Hatzfeld, O.M., Petersen, A., Link, T.A., Schaefer, G.
      (1997) Biochem Biophys Res Commun 234: 283

    Organizational Affiliation

    Department of Biosciences at NOVUM, Center for Structural Biochemistry, Karolinska Institutet, Hälsovägen 7-9, S-14157 Huddinge, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rieske iron-sulfur protein soxF A204Sulfolobus acidocaldariusMutation(s): 0 
Gene Names: soxFATY89_06800ATZ20_09820
Find proteins for Q53766 (Sulfolobus acidocaldarius)
Explore Q53766 
Go to UniProtKB:  Q53766
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.106 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.252α = 90
b = 80.252β = 90
c = 75.624γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance