9SIH image
Deposition Date 2025-08-28
Release Date 2026-05-13
Last Version Date 2026-06-17
Entry Detail
PDB ID:
9SIH
Keywords:
Title:
XFEL structure of Ribonucleotide reductase R2a Y122F mutant from E. coli,reduced form
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.19
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribonucleoside-diphosphate re
Gene (Uniprot):nrdB
Mutagens:Y122F
Chain IDs:A, B
Chain Length:375
Number of Molecules:2
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation

Abstact

Serial femtosecond crystallography (SFX) and continuous serial electron diffraction (c-SerialED) both enable high-resolution structure determination from protein microcrystals with minimal radiation damage, making it ideal for studying redox-active metalloenzymes. Here, c-SerialED and SFX were used to solve structures of the class Ia ribonucleotide reductase R2 subunit in oxidized (Fe(III)-Fe(III)), reduced (Fe(II)-Fe(II)), and re-oxidized states at approximately 1.8 A resolution, capturing three points in a redox reaction. These results demonstrate that c-SerialED can track reversible changes at the redox-site, enabling future time-resolved studies. Comparison between c-SerialED structures and SFX diffraction and emission data confirmed minimal radiation damage. Furthermore, previously reported structures use mercury in the crystallization condition and show mercury-induced conformational changes. Here, we use mercury-free crystallization conditions and reveal a water molecule in the redox center of the reduced state, absent in the previous structures, making these structures more representative of the physiological state.

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Primary Citation of related structures
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