1FDA

CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of oxidized and reduced Azotobacter vinelandii ferredoxin at pH 8 and 6.

Stout, C.D.

(1993) J.Biol.Chem. 268: 25920-25927

  • Primary Citation of Related Structures:  1FDB, 5FD1

  • PubMed Abstract: 
  • Crystal structures of Azotobacter vinelandii ferredoxin I (FdI) have been solved and refined at 2.2 to 1.9-A resolution at pH 8 and 6 for both the oxidized and dithionite-reduced proteins. Only the [3Fe-4S] cluster is reduced by dithionite. The four ...

    Crystal structures of Azotobacter vinelandii ferredoxin I (FdI) have been solved and refined at 2.2 to 1.9-A resolution at pH 8 and 6 for both the oxidized and dithionite-reduced proteins. Only the [3Fe-4S] cluster is reduced by dithionite. The four structures (denoted FdI8ox, FdI8red, FdI6ox, and FdI6red) have been compared to address three questions: the effect of reduction at pH 8, the effect of pH change on the structure, and the effect of reduction at pH 6. Comparison of the FdI8ox and FdI8red structures shows that Asp-15 changes conformation in a manner consistent with increased anionic repulsion between this residue and the reduced [3Fe-4S]0 cluster. By revealing an electrostatic interaction between Asp-15 and the [3Fe-4S] cluster, this result supports the conclusion in the accompanying paper (Shen, B., Martin, L. L., Butt, J. N., Armstrong, F. A., Stout, C. D., Jensen, G. M., Stephens, P. J., LaMar, G. N., Gorst, C. M., and Burgess, B. K. (1993) J. Biol. Chem. 268, 25928-25939) that Asp-15 participates in protonation of the reduced [3Fe-4S]0 cluster at acid pH. The [3Fe-4S]0 cluster in the FdI8red structure also displays a distinct shift within the protein as well as internal distortions when compared to the [3Fe-4S]+ cluster in the FdI8ox structure. Comparison of the FdI8ox and FdI6ox structures shows that pH change does not have any significant effect on the [3Fe-4S]+ cluster or surrounding residues. Comparison of the FdI6ox and FdI6red structures shows that reduction at pH 6 also does not have any significant effect on the [3Fe-4S] cluster or Asp-15. The absence of structural change supports the conclusion that at acid pH, the reduced [3Fe-4S] cluster is protonated, i.e. [3Fe-4S]0-H+ (Shen et al., 1993). The cluster is not shifted or distorted as in the FdI8red structure. Instead, the [3Fe-4S]o-H+ cluster FdI8red is structurally similar to the [3Fe-4S]+ cluster (FdI8ox, FdI6ox), which has the same net charge. An Asp-15-Lys-84 salt bridge is observed in all four structures, indicating that Asp-15 is ionized at pH 8 and 6. An ionized state for Asp-15 is also implied by a lack of conformational change in Lys-84; the side chain of this residue rearranges when Asp-15 is substituted with a neutral amino acid (Shen et al., 1993).(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • (4Fe-4S)-Cluster-Depleted Azotobacter Vinelandii Ferredoxin I. A New 3Fe Iron-Sulfur Protein
      Stephens, P.J.,Morgan, T.V.,Devlin, F.,Penner-Hahn, J.E.,Hodgson, K.O.,Scott, R.A.,Stout, C.D.,Burgess, B.K.
      (1985) Proc.Natl.Acad.Sci.USA 82: 5661
    • 7-Iron Ferredoxin Revisited
      Stout, C.D.
      (1988) J.Biol.Chem. 263: 9256
    • Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii
      Ghosh, D.,Fureyjunior, W.,O'Donnell, S.,Stout, C.D.
      (1981) J.Biol.Chem. 256: 4185
    • Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution
      Stout, C.D.,Ghosh, D.,Pattabhi, V.,Robbins, A.H.
      (1980) J.Biol.Chem. 255: 1797
    • Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Angstroms Resolution
      Ghosh, D.,O'Donnell, S.,Fureyjunior, W.,Robbins, A.H.,Stout, C.D.
      (1982) J.Mol.Biol. 158: 73
    • Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement
      Martin, A.E.,Burgess, B.K.,Stout, C.D.,Cash, V.L.,Dean, D.R.,Jensen, G.M.,Stephens, P.J.
      (1990) Proc.Natl.Acad.Sci.USA 87: 598
    • Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
      Stout, C.D.
      (1979) Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) 6: 97
    • Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin
      Soman, J.,Iismaa, S.,Stout, C.D.
      (1991) J.Biol.Chem. 266: 21558
    • Structure of Azotobacter Vinelandii 7Fe Ferredoxin. Amino Acid Sequence and Electron Density Maps of Residues
      Howard, J.B.,Lorsbach, T.W.,Ghosh, D.,Melis, K.,Stout, C.D.
      (1983) J.Biol.Chem. 258: 508
    • Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution
      Stout, C.D.
      (1989) J.Mol.Biol. 205: 545
    • Two Crystal Forms of Azotobacter Ferredoxin
      Stout, C.D.
      (1979) J.Biol.Chem. 254: 3598
    • Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
      Stout, C.D.
      (1979) Nature 279: 83


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
106Azotobacter vinelandiiGene Names: fdxA
Find proteins for P00214 (Azotobacter vinelandii)
Go to UniProtKB:  P00214
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: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.200α = 90.00
b = 55.200β = 90.00
c = 95.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-06-29 
  • Released Date: 1993-10-31 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance