2FDN

2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDI-URICI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein.

Dauter, Z.Wilson, K.S.Sieker, L.C.Meyer, J.Moulis, J.M.

(1997) Biochemistry 36: 16065-16073

  • DOI: 10.1021/bi972155y

  • PubMed Abstract: 
  • The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been solved using X-ray diffraction data extending to atomic resolution, 0.94 A, recorded at 100 K. The model was refined with anisotropic representation of atomic displ ...

    The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been solved using X-ray diffraction data extending to atomic resolution, 0.94 A, recorded at 100 K. The model was refined with anisotropic representation of atomic displacement parameters for all non-hydrogen atoms and with hydrogens riding on their parent atoms. Stereochemical restraints were applied to the protein chain but not to the iron-sulfur clusters. The final R factor is 10.03 % for all data. Inversion of the final least-squares matrix allowed direct estimation of the errors of individual parameters. The estimated errors in positions for protein main chain atoms are below 0.02 A and about 0.003 A for the heavier [4Fe-4S] cluster atoms. Significant differences between the stereochemistry of the two clusters and distortion of both of them from ideal Td tetrahedral symmetry can be defined in detail at this level of accuracy. Regions of alternative conformations include not only protein side chains but also two regions of the main chain. One such region is the loop of residues 25-29, which was highly disordered in the room temperature structure.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York, YO1 5DD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
55Clostridium acidurici (strain ATCC 7906 / DSM 604 / BCRC 14475 / CIP 104303 / NCIMB 10678 / 9a)Mutation(s): 0 
Gene Names: fdxA
Find proteins for P00198 (Clostridium acidurici (strain ATCC 7906 / DSM 604 / BCRC 14475 / CIP 104303 / NCIMB 10678 / 9a))
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: 0.94 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 33.950α = 90.00
b = 33.950β = 90.00
c = 74.820γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXmodel building
SHELXphasing
SHELXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance