1M2A

Crystal structure at 1.5 Angstroms resolution of the wild type thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus

Yeh, A.P.Ambroggio, X.I.Andrade, S.L.A.Einsle, O.Chatelet, C.Meyer, J.Rees, D.C.

(2002) J.Biol.Chem. 277: 34499-34507

  • DOI: 10.1074/jbc.M205096200
  • Primary Citation of Related Structures:  1M2B, 1M2D

  • PubMed Abstract: 
  • The [2Fe-2S] ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like polypeptide fold that is distinct from other [2Fe-2S] ferredoxins. Crystal structures of the Cys-55 --> Ser (C55S) and Cys-59 --> Ser (C59S) variants of this protein have b ...

    The [2Fe-2S] ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like polypeptide fold that is distinct from other [2Fe-2S] ferredoxins. Crystal structures of the Cys-55 --> Ser (C55S) and Cys-59 --> Ser (C59S) variants of this protein have been determined to 1.25 A and 1.05 A resolution, respectively, whereas the resolution of the wild type (WT) has been extended to 1.5 A. The improved WT structure provides a detailed description of the [2Fe-2S] cluster, including two features that have not been noted previously in any [2Fe-2S] cluster-containing protein, namely, pronounced distortions in the cysteine coordination to the cluster and a Calpha-H-Sgamma hydrogen bond between cluster ligands Cys-55 and Cys-9. These features may contribute to the unusual electronic and magnetic properties of the [2Fe-2S] clusters in WT and variants of this ferredoxin. The structures of the two variants of Fd4, in which single cysteine ligands to the [2Fe-2S] cluster are replaced by serine, establish the metric details of serine-ligated Fe-S active sites with unprecedented accuracy. Both the cluster and its surrounding protein matrix change in subtle ways to accommodate this ligand substitution, particularly in terms of distortions of the Fe(2)S(2) inorganic core from planarity and displacements of the polypeptide chain. These high resolution structures illustrate how the interactions between polypeptide chains and Fe-S active sites reflect combinations of flexibility and rigidity on the part of both partners; these themes are also evident in more complex systems, as exemplified by changes associated with serine ligation of the nitrogenase P cluster.


    Related Citations: 
    • Structure of a thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus
      Yeh, A.P.,Chatelet, C.,Soltis, S.M.,Kuhn, P.,Meyer, J.,Rees, D.C.
      (2000) J.Mol.Biol. 300: 587


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
[2Fe-2S] ferredoxin
A, B
110Aquifex aeolicus (strain VF5)Gene Names: fdx4
Find proteins for O66511 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66511
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FES
Query on FES

Download SDF File 
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: 1.5 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.200α = 90.00
b = 59.800β = 110.30
c = 47.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance