4DHV

Crystal structure of the Pyrococcus furiosus ferredoxin D14C variant containing the heterometallic [AgFe3S4] cluster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Heterometallic [AgFe(3)S (4)] ferredoxin variants: synthesis, characterization, and the first crystal structure of an engineered heterometallic iron-sulfur protein.

Martic, M.Jakab-Simon, I.N.Haahr, L.T.Hagen, W.R.Christensen, H.E.

(2013) J.Biol.Inorg.Chem. 18: 261-276

  • DOI: 10.1007/s00775-012-0971-3

  • PubMed Abstract: 
  • Heterometallic [AgFe(3)S(4)] iron-sulfur clusters assembled in wild-type Pyrococcus furiosus ferredoxin and two variants, D14C and D14H, are characterized. The crystal structure of the [AgFe(3)S(4)] D14C variant shows that the silver(I) ion is indeed ...

    Heterometallic [AgFe(3)S(4)] iron-sulfur clusters assembled in wild-type Pyrococcus furiosus ferredoxin and two variants, D14C and D14H, are characterized. The crystal structure of the [AgFe(3)S(4)] D14C variant shows that the silver(I) ion is indeed part of the cluster and is coordinated to the thiolate group of residue 14. Cyclic voltammetry shows one redox pair with a reduction potential of +220 mV versus the standard hydrogen electrode which is assigned to the [AgFe(3)S(4)](2+/+) couple. The oxidized form of the [AgFe(3)S(4)] D14C variant is stable in the presence of dioxygen, whereas the oxidized forms of the [AgFe(3)S(4)] wild type and D14H variants convert to the [Fe(3)S(4)] ferredoxin form. The monovalent d (10) silver(I) ion stabilizes the [Fe(3)S(4)](+/0) cluster fragment, as opposed to divalent d (10) metal ions, resulting in more than 0.4 V difference in reduction potentials between the silver(I) and, e.g., zinc(II) heterometallic [MFe(3)S(4)] ferredoxins. The trend in reduction potentials for the variants containing the [AgFe(3)S(4)] cluster is wild type ≤ D14C < D14H and shows the same trend as reported for the variants containing the [Fe(3)S(4)] cluster, but is different from the D14C < D14H < wild type trend reported for the [Fe(4)S(4)] ferredoxin. The similarity in the reduction potential trend for the variants containing the heterometallic [AgFe(3)S(4)] cluster and the [Fe(3)S(4)] cluster can be rationalized in terms of the electrostatic influence of the residue 14 side chains, rather than the dissociation constant of this residue, as is the case for [Fe(4)S(4)] ferredoxins. The trends in reduction potentials are in line with there being no electronic coupling between the silver(I) ion and the Fe(3)S(4) fragment.


    Organizational Affiliation

    Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferredoxin
B, A
66Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Gene Names: fdxA
Find proteins for P29603 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  P29603
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A, B
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
0KA
Query on 0KA

Download SDF File 
Download CCD File 
A, B
SILVER/IRON/SULFUR CLUSTER
Ag Fe3 S4
FVQUTMRPEYETPT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.110α = 90.00
b = 49.330β = 90.00
c = 54.390γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references
  • Version 1.2: 2013-03-06
    Type: Database references