1FD2

SITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I. (FE-S) CLUSTER-DRIVEN PROTEIN REARRANGEMENT

• PDB DOI: https://doi.org/10.2210/pdb1FD2/pdb

• Classification: ELECTRON TRANSFER(IRON-SULFUR PROTEIN)
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 1988-12-08 Released: 1989-10-15 
• Deposition Author(s): Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 
  0.232 (Depositor) 

Literature

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 U S A 87: 598-602

• PubMed: 2153958 
• DOI: https://doi.org/10.1073/pnas.87.2.598
• Primary Citation of Related Structures:  
  1FD2


• PubMed Abstract: 
  

  Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced. Here we report the site-directed mutation of Cys-20, which is a ligand of the [4Fe-4S] cluster in the native protein, to alanine and the characterization of the protein product by x-ray crystallographic and spectroscopic methods. The data show that the mutant protein again contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. The new [4Fe-4S] cluster obtains its fourth ligand from Cys-24, a free cysteine in the native structure. The formation of this [4Fe-4S] cluster drives rearrangement of the protein structure.

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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, University of California, Irvine 92717.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.67 kDa 
• Atom Count: 886 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERREDOXIN	A	106	Azotobacter vinelandii	Mutation(s): 0
UniProt
Find proteins for P00214 (Azotobacter vinelandii) Explore P00214  Go to UniProtKB:  P00214

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	C [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work:  0.232 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55	α = 90
b = 55	β = 90
c = 95.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1989-10-15 
Deposition Author(s): Stout, C.D.

Revision History  

• Version 1.0: 1989-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other