1FER

STRUCTURE AT PH 6.5 OF FERREDOXIN I FROM AZOTOBACTER VINELANDII AT 2.3 ANGSTROMS RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.170 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure at pH 6.5 of ferredoxin I from Azotobacter vinelandii at 2.3 A resolution.

Merritt, E.A., Stout, G.H., Turley, S., Sieker, L.C., Jehsen, L.H., Orme-Johnson, W.H.

(1993) Acta Crystallogr D Biol Crystallogr 49: 272-281

  • DOI: 10.1107/S0907444992007248
  • Primary Citation of Related Structures:  
    1FER

  • PubMed Abstract: 

    • Ferredoxin I from Azotobacter vinelandii (AvFdI) is an iron-sulfur protein composed of 106 amino acids, seven Fe atoms and eight inorganic S* atoms. A crystallographic redetermination of its structure showed the originally reported structure to be in ...

    Ferredoxin I from Azotobacter vinelandii (AvFdI) is an iron-sulfur protein composed of 106 amino acids, seven Fe atoms and eight inorganic S* atoms. A crystallographic redetermination of its structure showed the originally reported structure to be incorrect. We report here the crystal structure of AvFdI at pH 6.5. Extensive refinement has led to a final R value of 0.170 for all 6986 non-extinct reflections in the range 10-2.3 A using a solvent model which includes 98 discrete solvent atoms with occupancies between 0.3 and 1.0 and an average B value of 22.5 A(2). The first half of the peptide chain closely resembles that of the 55-residue ferredoxin from Peptococcus aerogenes (PaFd), while the remainder consists of three turns of helix and a series of loops which form a cap over part of the molecular core. Despite the similarities in structure and surroundings, the corresponding 4Fe4S* clusters in PaFd and AvFdI have strikingly different redox potentials; a possible explanation has been sought in the differing hydration models for the two molecules.

    Related Citations: 
    • Structure of Ferredoxin I from Azotobacter Vinelandii
      Stout, G.H., Turley, S., Sieker, L.C., Jensen, L.H.
      (1988) Proc Natl Acad Sci U S A 85: 1020
    Organizational Affiliation: 

    Department of Biological Structure, University of Washington, Seattle 98195, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERREDOXIN IA106Azotobacter vinelandiiMutation(s): 0 
Gene Names: fdxA
Find proteins for P00214 (Azotobacter vinelandii)
Explore P00214 
Go to UniProtKB:  P00214
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
Download Ideal Coordinates CCD File 
A
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.55α = 90
b = 55.55β = 90
c = 95.65γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance