1GAO

CRYSTAL STRUCTURE OF THE L44S MUTANT OF FERREDOXIN I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential.

Chen, K., Jung, Y.S., Bonagura, C.A., Tilley, G.J., Prasad, G.S., Sridhar, V., Armstrong, F.A., Stout, C.D., Burgess, B.K.

(2002) J.Biol.Chem. 277: 5603-5610

  • DOI: 10.1074/jbc.M108916200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The reduction potential (E(0)') of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I (AvFdI) and related ferredoxins is approximately 200 mV more negative than the corresponding clusters of Peptostreptococcus asaccharolyticus ferredox ...

    The reduction potential (E(0)') of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I (AvFdI) and related ferredoxins is approximately 200 mV more negative than the corresponding clusters of Peptostreptococcus asaccharolyticus ferredoxin and related ferredoxins. Previous studies have shown that these differences in E(0)' do not result from the presence or absence of negatively charged surface residues or in differences in the types of hydrophobic residues found close to the [4Fe-4S](2+/+) clusters. Recently, a third, quite distinct class of ferredoxins (represented by the structurally characterized Chromatium vinosum ferredoxin) was shown to have a [4Fe-4S](2+/+) cluster with a very negative E(0)' similar to that of AvFdI. The observation that the sequences and structures surrounding the very negative E(0)' clusters in quite dissimilar proteins were almost identical inspired the construction of three additional mutations in the region of the [4Fe-4S](2+/+) cluster of AvFdI. The three mutations, V19E, P47S, and L44S, that incorporated residues found in the higher E(0)' P. asaccharolyticus ferredoxin all led to increases in E(0)' for a total of 130 mV with a 94-mV increase in the case of L44S. The results are interpreted in terms of x-ray structures of the FdI variants and show that the major determinant for the large increase in L44S is the introduction of an OH-S bond between the introduced Ser side chain and the Sgamma atom of Cys ligand 42 and an accompanying movement of water.

    Organizational Affiliation: 

    Department of Molecular Biology and Biochemistry and Irvine Research Unit in Macromolecular Structure, University of California, Irvine, California 92697, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN I
A, B, C, D
106Azotobacter vinelandiiMutation(s): 1 
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, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S
Download SDF File 
Download CCD File 
A, B, C, D
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.800α = 90.00
b = 85.600β = 117.90
c = 67.200γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
MAR345data collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description