1CLF

CLOSTRIDIUM PASTEURIANUM FERREDOXIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 16 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum.

Bertini, I.Donaire, A.Feinberg, B.A.Luchinat, C.Piccioli, M.Yuan, H.

(1995) Eur.J.Biochem. 232: 192-205


  • PubMed Abstract: 
  • Following the recently developed approach to the solution structure of paramagnetic high-potential iron-sulfur proteins, the three-dimensional structure in solution of the oxidized Clostridium pasteurianum ferredoxin has been solved by 1H-NMR. The X- ...

    Following the recently developed approach to the solution structure of paramagnetic high-potential iron-sulfur proteins, the three-dimensional structure in solution of the oxidized Clostridium pasteurianum ferredoxin has been solved by 1H-NMR. The X-ray structure is not available. The protein contains 55 amino acids and two [4Fe-4S] clusters. In the oxidized state, the clusters have S = 0 ground states, but are paramagnetic because of thermal population of excited states. Due to the somewhat small size of the protein and to the presence of two clusters, approximately 55% of the residues have at least one proton with a non-selective T1 smaller than 25 ms. The protein has thus been used as a test system to challenge the present paramagnetic NMR methodology both in achieving an extended assignment and in obtaining a suitable number of constraints. 79% of protein protons have been assigned. Analogy with other ferredoxins of known structure has been of help to speed up the final stages of the assignment, although we have shown that this independent information is not necessary. In addition to dipolar connectivities, partially detected through tailored experiments, 3JHN-H alpha, H-bond constraints and dihedral angle constraints on the Cys chi 2 angles have been generated by using a recently derived Karplus-type relationship for the hyperfine shifts of cysteine beta CH2 protons. In total, 456 constraints have been used in distance geometry calculations. The final quality of the structures is satisfactory, with root-mean-square deviation values of 66 pm and 108 pm for backbone and heavy atoms, respectively. The resulting structure is compared with that of Clostridium acidi urici ferredoxin [Duée, E. D., Fanchon, E., Vicat, J., Sieker, L. C., Meyer, J. & Moulis, J.-M. (1994) J. Mol. Biol. 243, 683-695]. The two proteins are very similar in the overall folding, secondary structure elements and side-chain orientations. The C alpha root-mean-square deviation values between the X-ray-determined C. acidi urici ferredoxin structure and the conformer with lowest energy of the C. pasteurianum ferredoxin family is 78 pm (residues 3-53). Discrepancies in residues 26-28 may arise from the disorder observed in the X-ray structure in that region.


    Related Citations: 
    • The Fe4S4 Centers in Ferredoxins Studied Through Proton and Carbon Hyperfine Coupling. Sequence Specific Assignments of Cysteines in Ferredoxins from Clostridium Acidi Urici and Clostridium Pasteurianum
      Bertini, I.,Cappozzi, F.,Luchinat, C.,Piccioli, M.,Vila, A.J.
      (1994) J.Am.Chem.Soc. 116: 651
    • Preparation and Properties of Clostridial Ferredoxins
      Rabinowitz, J.
      (1972) Methods Enzymol. 24: 431
    • Comparison of Native and Mutant Proteins Provides a Sequence-Specific Assignment of the Cysteinyl Ligand Proton NMR Resonances in the 2[Fe4S4] Ferredoxin from Clostridium Pasteurianum
      Scrofani, S.D.B.,Brereton, P.S.,Hamer, A.M.,Lavery, M.J.,Mcdowall, S.G.,Vincent, G.A.,Brownlee, R.T.C.,Hoogenraad, N.J.,Sadek, M.,Wedd, A.G.
      (1994) Biochemistry 33: 14486


    Organizational Affiliation

    Department of Chemistry, University of Florence, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
55Clostridium pasteurianumN/A
Find proteins for P00195 (Clostridium pasteurianum)
Go to UniProtKB:  P00195
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: SOLUTION NMR
  • Conformers Submitted: 16 
  • Olderado: 1CLF Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance