1BD6

7-FE FERREDOXIN FROM BACILLUS SCHLEGELII, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium Bacillus schlegelii by 1H NMR spectroscopy.

Aono, S.Bentrop, D.Bertini, I.Donaire, A.Luchinat, C.Niikura, Y.Rosato, A.

(1998) Biochemistry 37: 9812-9826

  • DOI: 10.1021/bi972818b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The solution structure of the paramagnetic seven-iron ferredoxin from Bacillus schlegelii in its oxidized form has been determined by 1H NMR. The protein, which contains 77 amino acids, is thermostable. Seventy-two residues and 79% of all theoretical ...

    The solution structure of the paramagnetic seven-iron ferredoxin from Bacillus schlegelii in its oxidized form has been determined by 1H NMR. The protein, which contains 77 amino acids, is thermostable. Seventy-two residues and 79% of all theoretically expected proton resonances have been assigned. The structure has been determined through torsion angle dynamics calculations with the program DYANA, using 966 meaningful NOEs (from a total of 1305), hydrogen bond constraints, and NMR derived dihedral angle constraints for the cluster ligating cysteines, and by using crystallographic information to build up the two clusters. Afterwards, restrained energy minimization and restrained molecular dynamics were applied to each conformer of the family. The final family of 20 structures has RMSD values from the mean structure of 0.68 A for the backbone atoms and of 1.16 A for all heavy atoms. The contributions to the thermal stability of the B. schlegelii ferredoxin are discussed by comparing the present structure to that of the less stable Azotobacter vinelandii ferredoxin I which is the only other available structure of a bacterial seven-iron ferredoxin. It is proposed that the hydrophobic interactions and the hydrogen bond network linking the N-terminus and the C-terminus together and a high number of salt bridges contribute to the stability.


    Related Citations: 
    • Purification and Characterization of a 7Fe Ferredoxin from a Thermophilic Hydrogen-Oxidizing Bacterium, Bacillus Schlegelii
      Aono, S.,Kurita, H.,Uno, S.,Okura, I.
      (1992) J.Biochem.(Tokyo) 112: 792
    • 1H NMR Studies of the Fe7S8 Ferredoxin from Bacillus Schlegelii: A Further Attempt to Understand Fe3S4 Clusters
      Aono, S.,Bertini, I.,Cowan, J.A.,Luchinat, C.,Rosato, A.,Viezzoli, M.S.
      (1996) J.Biol.Inorg.Chem. 1: 523
    • Cloning and Expression of the Gene Encoding the 7Fe Type Ferredoxin from a Thermophilic Hydrogen Oxidizing Bacterium, Bacillus Schlegelii
      Aono, S.,Nakamura, S.,Aono, R.,Okura, I.
      (1994) Biochem.Biophys.Res.Commun. 201: 938


    Organizational Affiliation

    School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7-FE FERREDOXIN
A
77Hydrogenibacillus schlegeliiMutation(s): 0 
Gene Names: fdxA
Find proteins for Q45560 (Hydrogenibacillus schlegelii)
Go to UniProtKB:  Q45560
Small Molecules
Ligands 2 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
F3S
Query on F3S

Download SDF File 
Download CCD File 
A
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 
Software Package:
Software NamePurpose
DYANArefinement
AMBERrefinement
DYANAmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance