1FRR

CRYSTAL STRUCTURE OF [2FE-2S] FERREDOXIN I FROM EQUISETUM ARVENSE AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of [2Fe-2S] ferredoxin I from Equisetum arvense at 1.8 A resolution.

Ikemizu, S.Bando, M.Sato, T.Morimoto, Y.Tsukihara, T.Fukuyama, K.

(1994) Acta Crystallogr D Biol Crystallogr 50: 167-174

  • DOI: 10.1107/S0907444993009588
  • Primary Citation of Related Structures:  
    1FRR

  • PubMed Abstract: 
  • Ferredoxin I (Fd I) from Equisetum arvense is an iron-sulfur protein composed of 95 amino-acid residues and one [2Fe-2S] cluster. It crystallized in the space group P2(1), a = 30.4, b = 57.4, c = 47.5 A and beta = 78.7 degrees with two molecules per ...

    Ferredoxin I (Fd I) from Equisetum arvense is an iron-sulfur protein composed of 95 amino-acid residues and one [2Fe-2S] cluster. It crystallized in the space group P2(1), a = 30.4, b = 57.4, c = 47.5 A and beta = 78.7 degrees with two molecules per asymmetric unit. X-ray diffraction data up to 1.8 A resolution were collected by using a Rigaku four-circle diffractometer. The initial model of Fd I, which was derived by the molecular replacement method using a structure of the Fd I from the blue-green alga Aphanothece sacrum, was refined by molecular dynamics simulation and a least-squares minimization with stereochemical restraints. Positional parameters and isotropic temperature factors for 1420 non-H protein atoms and 183 water molecules were refined on 13 838 observed structure factors (F(o) > sigma(Fo)) between 10.0 and 1.8 A resolution. The final Rfactor was 17.0%, and the standard deviation of atomic position estimated by Luzzati plot [Luzzati (1952). Acta Cryst. 5, 802-810] was 0.2 A. The electron-density map was well defined for the two independent molecules except for the N-terminal residue and the three C-terminal residues. Equivalent Calpha atoms of two independent molecules in the asymmetric unit were superposed by the least-squares method with root-mean-square deviations of 0.26 A. Reasonable structural differences were observed at a polypeptide segment having few intramolecular interactions. Highly flexible regions of the molecule were assigned from the structural differences between the two independent molecules in the crystal and the distribution of temperature factors along the polypeptide chain.


    Organizational Affiliation

    The Graduate University for Advanced Studies, Oho, Tsukuba, Ibaraki, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERREDOXIN IAB95Equisetum arvenseMutation(s): 0 
Find proteins for P00235 (Equisetum arvense)
Explore P00235 
Go to UniProtKB:  P00235
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 CCD File 
A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.4α = 90
b = 57.4β = 78.7
c = 47.5γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1993-09-24 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Tsukihara, T.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance