1FXI

STRUCTURE OF THE [2FE-2S] FERREDOXIN I FROM THE BLUE-GREEN ALGA APHANOTHECE SACRUM AT 2.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the [2Fe-2S] ferredoxin I from the blue-green alga Aphanothece sacrum at 2.2 A resolution.

Tsukihara, T.Fukuyama, K.Mizushima, M.Harioka, T.Kusunoki, M.Katsube, Y.Hase, T.Matsubara, H.

(1990) J.Mol.Biol. 216: 399-410

  • DOI: 10.1016/S0022-2836(05)80330-4

  • PubMed Abstract: 
  • Crystals of a [2Fe-2S] ferredoxin (Fd) I with a relative molecular mass of 10,480 were obtained from the blue-green alga Aphanothece sacrum. Each asymmetric unit of the crystal contains four molecules. An electron density map calculated by the single ...

    Crystals of a [2Fe-2S] ferredoxin (Fd) I with a relative molecular mass of 10,480 were obtained from the blue-green alga Aphanothece sacrum. Each asymmetric unit of the crystal contains four molecules. An electron density map calculated by the single isomorphous replacement method with the anomalous dispersion at 2.5 A resolution was refined by averaging the four molecules in the asymmetric unit. Positional and isotropic thermal parameters for the non-hydrogen atoms of the four molecules and 158 water molecules were refined to an R-factor (R = sigma[Fo-Fc[/sigma Fo) of 0.23 by the restrained least-squares method. The estimated root-mean-square (r.m.s.) error for the atomic positions is 0.3 A. The r.m.s. deviations of equivalent C alpha atoms of the asymmetric-unit molecules superposed by the least-squares method average 0.35 A. The Fd molecule has a structure like the beta-barrel in the molecule of the [2Fe-2S] Fd from Spirulina platensis. A [2Fe-2S] cluster is bonded covalently to the protein molecule by four Fe-S, in which three of the Fe-S bonds are in a loop segment from position 38 to 47. The hydrophobic core inside the beta-barrel is formed by seven conservative residues: Val15, Val18, Ile24, Leu51, Ile74, Ala79 and Ile87. The molecular surface around Tyr23, Tyr80 and the active center may interact with ferredoxin-NADP+ reductase. One of the two iron atoms of the [2Fe-2S] cluster should be more easily reduced than the other because of differences in the hydrogen-bonding scheme and the hydrophobicity around the atoms.


    Related Citations: 
    • Crystallization and a 5 Angstroms X-Ray Diffraction Study of Aphanothece Sacrum Ferredoxin
      Kunita, A.,Koshibe, M.,Nishikawa, Y.,Fukuyama, K.,Tsukihara, T.,Katsube, Y.,Matsuura, Y.,Tanaka, N.,Kakudo, M.,Hase, T.,Matsubara, H.
      (1978) J.Biochem.(Tokyo) 84: 989
    • Main Chain Fold of a [2Fe-2S] Ferredoxin I from Aphanothece Sacrum at 2.5 Angstroms Resolution
      Tsutsui, T.,Tsukihara, T.,Fukuyama, K.,Katsube, Y.,Hase, T.,Matsubara, H.,Nishikawa, Y.,Tanaka, N.
      (1983) J.Biochem.(Tokyo) 94: 299


    Organizational Affiliation

    Faculty of Engineering, Tottori University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN I
A, B, C, D
96Aphanothece sacrumN/A
Find proteins for P00250 (Aphanothece sacrum)
Go to UniProtKB:  P00250
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 92.200α = 90.00
b = 92.200β = 90.00
c = 47.600γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1990-08-28 
  • Released Date: 1991-10-15 
  • Deposition Author(s): Tsukihara, T.

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance