1FDN

REFINED CRYSTAL STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDURICI AT 1.84 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution.

Duee, E.D.Fanchon, E.Vicat, J.Sieker, L.C.Meyer, J.Moulis, J.M.

(1994) J.Mol.Biol. 243: 683-695


  • PubMed Abstract: 
  • The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been determined at a resolution of 1.84 A and refined to an R-factor of 0.169. Crystals belong to space group P4(3)2(1)2 with unit cell dimensions a = b = 34.44 A and c ...

    The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been determined at a resolution of 1.84 A and refined to an R-factor of 0.169. Crystals belong to space group P4(3)2(1)2 with unit cell dimensions a = b = 34.44 A and c = 74.78 A. The structure was determined by molecular replacement using the previously published model of an homologous ferredoxin and refined by molecular dynamics techniques. The model contains the protein and 46 water molecules. Only two amino acid residues, Asp27 and Asp28, are poorly defined in the electron density maps. The molecule has an overall chain fold similar to that of other [4Fe-4S] bacterial ferredoxins of known structure. The two [4Fe-4S] clusters display similar bond distances and angles. In both of them the co-ordination of one iron atom (bound to Cys11 and Cys40) is slightly distorted as compared with that of the other iron atoms. A core of hydrophobic residues and a few water molecules contribute to the stability of the structure. The [4Fe-4S] clusters interact with the polypeptide chain through eight hydrogen bonds each, in addition to the covalent Fe-Scys bonds. The ferredoxin from Clostridium acidurici is the most typical clostridial ferredoxin crystallized so far and the biological implications of the newly determined structure are discussed.


    Related Citations: 
    • Crystal Structure of Clostridium Acidi-Urici Ferredoxin at 5 Angstroms Resolution Based on Measurements of Anomalous X-Ray Scattering at Multiple Wavelengths
      Krishnamurthy, H.M.,Hendrickson, W.A.,Orme-Johnson, W.H.,Merritt, E.A.,Phizackerley, R.P.
      (1988) J.Biol.Chem. 263: 18430
    • Sequences of Clostridial Ferredoxins
      Meyer, J.,Moulis, J.-M.,Scherrer, N.,Gagnon, J.,Ulrich, J.
      (1993) Biochem.J. 294: 622


    Organizational Affiliation

    Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
55Clostridium aciduriciN/A
Find proteins for P00198 (Clostridium acidurici)
Go to UniProtKB:  P00198
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 34.440α = 90.00
b = 34.440β = 90.00
c = 74.780γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance