2VKR

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.273 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

Frazao, C.Aragao, D.Coelho, R.Leal, S.S.Gomes, C.M.Teixeira, M.Carrondo, M.A.

(2008) FEBS Lett 582: 763-767

  • DOI: 10.1016/j.febslet.2008.01.041
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A ...

    Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn(2+) site and the ferredoxin (betaalphabeta)(2) core, which harbours intact clusters I and II, a [3Fe-4S](1+/0) and a [4Fe-4S](2+/1+) centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe-4S](1+/0) centres and poor definition around cluster II.


    Related Citations: 
    • A Spectroscopic Study of the Temperature Induced Modifications on Ferredoxin Folding and Iron-Sulfur Moieties
      Todorovic, S., Leal, S.S., Salgueiro, C.A., Zebger, I., Hildebrandt, P., Murgida, D.H., Gomes, C.M.
      (2007) Biochemistry 46: 10733
    • Studies of the Molten Globule State of Ferredoxin: Structural Characterisation and Implications on Protein Folding and Iron-Sulfur Centre Assembly
      Leal, S.S., Gomes, C.M.
      (2007) Proteins 68: 606
    • Natural Domain Design: Enhanced Thermal Stability of a Zinc Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site
      Rocha, R., Leal, S., Teixeira, M., Regalla, M., Huber, H., Baptista, A., Soares, C.M., Gomes, C.M.
      (2006) Biochemistry 45: 10376
    • ,Di-Cluster, Seven-Iron Ferredoxins from Hyperthermophilic Sulfolobales
      Gomes, C.M., Faria, A., Carita, J.C., Mendes, J., Regalla, M., Chicau, P., Huber, H., Stetter, K.O., Teixeira, M.
      (1998) J Biol Inorg Chem 3: 499
    • A Seven Iron Ferredoxin from the Thermoacidophilic Archaeon Desulfurolobus Ambivalens
      Teixeira, M., Batista, R., Campos, A., Gomes, C., Mendes, J., Pacheco, I., Anemuller, S., Hagen, W.
      (1995) Eur J Biochem 217: 322

    Organizational Affiliation

    Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av da República, Oeiras, Portugal. frazao@itqb.unl.pt



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ZINC-CONTAINING FERREDOXIN
A, B, C, D, E, F, G
103Acidianus ambivalensMutation(s): 0 
Gene Names: zfx
Find proteins for P49949 (Acidianus ambivalens)
Go to UniProtKB:  P49949
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download CCD File 
A, B, C, D, E, F, G
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
A, B, C, D, E, F, G
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D, E, F, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.273 
  • R-Value Observed: 0.220 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.5α = 90
b = 117.5β = 90
c = 50.9γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description