2FD2

CRYSTALLOGRAPHIC ANALYSIS OF TWO SITE-DIRECTED MUTANTS OF AZOTOBACTER VINELANDII FERREDOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analysis of two site-directed mutants of Azotobacter vinelandii ferredoxin.

Soman, J.Iismaa, S.Stout, C.D.

(1991) J.Biol.Chem. 266: 21558-21562


  • PubMed Abstract: 
  • The crystal structure of the C24A mutant of Azotobacter vinelandii 7Fe ferredoxin (FdI) has been solved and refined at 2.0-A resolution. The structure is isomorphous to native FdI except at the site of mutation where A24 moves toward the [4Fe-4S] clu ...

    The crystal structure of the C24A mutant of Azotobacter vinelandii 7Fe ferredoxin (FdI) has been solved and refined at 2.0-A resolution. The structure is isomorphous to native FdI except at the site of mutation where A24 moves toward the [4Fe-4S] cluster. In spite of this inefficient packing results: three of five van der Waals contacts from the S gamma of C24 in native FdI are lost and the remaining two become longer. Consequently, the [4Fe-4S] cluster is either disordered or has a higher temperature factor (B factor) compared to the rest of the C24A FdI molecule. In addition, the entire C24A FdI structure has a higher overall B factor than native FdI. Therefore, in comparison to native FdI, the C24A mutant is isomorphous but exhibits large differences in B factor, especially at the [4Fe-4S] cluster. In contrast, the C20A FdI structure (Martin, A. G., Burgess, B. K., Stout, C. D., Cash, V. L., Dean, D. R., Jensen, G. M., and Stephens, P. J. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 598-602), which contains large structural rearrangements in the vicinity of the [4Fe-4S] cluster, exhibits essentially no change in B factor. The conformational change observed at residue 24 is similar in both C24A and C20A FdI structures. The solvent accessibility of the Fe atoms in the [3Fe-4S] and [4Fe-4S] clusters is similar in C24A, C20A, and native FdI.


    Related Citations: 
    • 7-Iron Ferredoxin Revisited
      Stout, C.D.
      (1988) J.Biol.Chem. 263: 9256
    • Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
      Stout, C.D.
      (1979) Nature 279: 83
    • 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
    • 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
    • Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution
      Stout, C.D.
      (1989) J.Mol.Biol. 205: 545
    • 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
    • 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
    • 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
    • (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
    • Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii
      Ghosh, D.,Fureyjunior, W.,O'Donnell, S.,Stout, C.D.
      (1981) J.Biol.Chem. 256: 4185
    • Two Crystal Forms of Azotobacter Ferredoxin
      Stout, C.D.
      (1979) J.Biol.Chem. 254: 3598


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
106Azotobacter vinelandiiMutation(s): 0 
Gene 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: 1.9 Å
  • R-Value Work: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.200α = 90.00
b = 55.200β = 90.00
c = 95.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1990-08-20 
  • Released Date: 1990-10-15 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance