4FXC

TERTIARY STRUCTURE OF [2FE-2S] FERREDOXIN FROM SPIRULINA PLATENSIS REFINED AT 2.5 ANGSTROMS RESOLUTION: STRUCTURAL COMPARISONS OF PLANT-TYPE FERREDOXINS AND AN ELECTROSTATIC POTENTIAL ANALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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This is version 1.2 of the entry. See complete history


Literature

Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 A resolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis.

Fukuyama, K.Ueki, N.Nakamura, H.Tsukihara, T.Matsubara, H.

(1995) J Biochem 117: 1017-1023

  • DOI: 10.1093/oxfordjournals.jbchem.a124800
  • Primary Citation of Related Structures:  
    4FXC

  • PubMed Abstract: 
  • The structure of plant-type [2Fe-2S] ferredoxin isolated from Spirulina platensis has been refined using diffraction data to 2.5 A resolution by alternate cycles of simulated annealing and manual revision of the model. The final R factor is 19.9% for 2,912 reflections with F > 2 sigma F between 8 ...

    The structure of plant-type [2Fe-2S] ferredoxin isolated from Spirulina platensis has been refined using diffraction data to 2.5 A resolution by alternate cycles of simulated annealing and manual revision of the model. The final R factor is 19.9% for 2,912 reflections with F > 2 sigma F between 8.0 and 2.5 A resolution. S. platensis ferredoxin, like other plant-type [2Fe-2S] ferredoxins, has a major alpha-helix flanking a sheet consisting of four beta strands. The present refinement revises the conformation of residues 56-71, in which a one-turn helix was identified. Superposition of the Spirulina ferredoxin structure on the structures of other ferredoxins that have been well refined showed structural perturbation at a few residues on the amino and carboxyl termini and the turn between the first and second beta-strands. The root-mean-square deviations of the corresponding C alpha atoms of the pairs of ferredoxins range from 0.90 to 1.17 A for all the residues, but from 0.64 to 0.70 A if the few perturbed residues are excluded. Therefore, it may be concluded that the main-chain foldings of all the plant-type [2Fe-2S] ferredoxins are essentially the same. Electrostatic potential analysis showed that the molecular surface around the cluster is negatively charged, whereas that of the beta-sheet of the other side is positively charged. The interaction between ferredoxin and ferredoxin-NADP+ reductase is discussed on the basis of the charge distributions of these molecules and biochemical data.


    Related Citations: 
    • X-Ray Analysis of a (2Fe-2S) Ferredoxin from Spirulina Platensis. Main Chain Fold and Location of Side Chains at 2.5 Angstroms Resolution
      Tsukihara, T., Fukuyama, K., Nakamura, M., Katsube, Y., Tanaka, N., Kakudo, M., Wada, K., Hase, T., Matsubara, H.
      (1981) J Biochem 90: 1763
    • Structure of S. Platensis (2Fe-2S) Ferredoxin and Evolution of Chloroplast-Type Ferredoxins
      Fukuyama, K., Hase, T., Matsumoto, S., Tsukihara, T., Katsube, Y., Tanaka, N., Kakudo, M., Wada, K., Matsubara, H.
      (1980) Nature 286: 522
    • X-Ray Analysis of Ferredoxin from Spirulina Platensis. II. Chelate Structure of Active Center
      Tsukihara, T., Fukuyama, K., Tahara, H., Katsube, Y., Matsuura, Y., Tanaka, N., Kakudo, M., Wada, K., Matsubara, H.
      (1978) J Biochem 84: 1645
    • Location of the Iron-Sulfur Cluster in Spirulina Platensis Ferredoxin by X-Ray Analysis
      Ogawa, K., Tsukihara, T., Tahara, H., Katsube, Y., Matsu-Ura, Y., Tanaka, N., Kakudo, M., Wada, K., Matsubara, H.
      (1977) J Biochem 81: 529

    Organizational Affiliation

    Department of Biology, Faculty of Science, Osaka University.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERREDOXINA98Arthrospira platensisMutation(s): 0 
UniProt
Find proteins for P00246 (Arthrospira platensis)
Explore P00246 
Go to UniProtKB:  P00246
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.32α = 90
b = 28.51β = 90
c = 108.08γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance