2FD2 | pdb_00002fd2

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

• PDB DOI: https://doi.org/10.2210/pdb2FD2/pdb

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


• Deposited: 1990-08-20 Released: 1990-10-15 
• 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

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

Soman, J., Iismaa, S., Stout, C.D.

(1991) J Biological Chem 266: 21558-21562

• PubMed: 1939185 
• Primary Citation Related Structures: 
  2FD2


• 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] 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.

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Organizational Affiliation: 
• Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California 92037.

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: 885 
• Modeled 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 = 55.2	α = 90
b = 55.2	β = 90
c = 95.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other