7PPU image
Deposition Date 2021-09-15
Release Date 2022-06-08
Last Version Date 2024-01-31
Entry Detail
PDB ID:
7PPU
Title:
Structure of diFe-Sulerythrin at 0.57 MGy total absorbed dose
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.34 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 63
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Sulerythrin
Gene (Uniprot):ST2370
Chain IDs:A, B
Chain Length:145
Number of Molecules:2
Biological Source:Sulfurisphaera tokodaii str. 7
Primary Citation
Determining the oxidation state of elements by X-ray crystallography.
Acta Crystallogr D Struct Biol 78 238 247 (2022)
PMID: 35102889 DOI: 10.1107/S2059798321013048

Abstact

Protein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron-sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron-sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H2O2. Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis.

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