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Structure of Peptococcus aerogenes ferredoxin. Refinement at 2 A resolution

E T Adman, L C Siefker, L H Jensen

The Journal of Biological Chemistry

|June 25, 1976

Summary

This study refined the ferredoxin model from Peptococcus aerogenes using high-resolution data, significantly improving structural accuracy. The refined model provides a detailed atomic view of this important iron-sulfur protein.

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Area of Science:

Biochemistry
Structural Biology
X-ray Crystallography

Background:

Ferredoxins are crucial electron transport proteins containing iron-sulfur clusters.
Understanding ferredoxin structure is vital for deciphering biological redox processes.

Purpose of the Study:

To refine the three-dimensional atomic model of ferredoxin from Peptococcus aerogenes.
To enhance the resolution and accuracy of the ferredoxin structural model.

Main Methods:

X-ray crystallography was used to obtain diffraction data.
The initial 2.8-Å resolution model was refined using a 2-Å resolution dataset.
Computational methods were employed for model refinement and validation.

Main Results:

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The crystallographic R-factor was reduced from 0.449 to 0.188 (unconstrained) and 0.206 (constrained).
Atomic positional uncertainties were determined, with iron and sulfur atoms showing high precision (0.04–0.05 Å).
146 water molecules were identified and validated in the solvent structure.

Conclusions:

The refined ferredoxin model offers an accurate atomic representation of the protein.
This detailed structure facilitates further investigation into ferredoxin's function in electron transfer.
The validation of water molecules enhances the understanding of the protein's hydration shell.