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: 2.5 Å
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


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.(Tokyo) 117: 1017-1023


  • 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 ...

    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 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.(Tokyo) 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.(Tokyo) 81: 529
    • 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 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.(Tokyo) 90: 1763


    Organizational Affiliation

    Department of Biology, Faculty of Science, Osaka University.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
98Arthrospira platensisMutation(s): 0 
Find proteins for P00246 (Arthrospira platensis)
Go to UniProtKB:  P00246
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.320α = 90.00
b = 28.510β = 90.00
c = 108.080γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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