9TCE

XFEL structure of Ribonucleotide reductase R2a Y122F mutant from E. coli,reduced form, hexagonal P6122

Summary for 9TCE

• Entry DOI: 10.2210/pdb9tce/pdb
• Descriptor: Ribonucleoside-diphosphate reductase 1 subunit beta, FE (II) ION (3 entities in total)
• Functional Keywords: ribonucleotide reductase beta subunit, r2a, di-iron beta subunit, reduced r2a, xfel structure, oxidoreductase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 43522.55

Authors

Kumar, R.,Srinivas, V.,Hogbom, M. (deposition date: 2025-11-21, release date: 2026-05-13, Last modification date: 2026-05-20)

Primary citation

Pacoste, L.,Kumar, R.,Srinivas, V.,Makita, H.,Simon, P.S.,Bannerjee, R.,Minnetian, N.M.,Bhowmick, A.,Paley, D.W.,Mittan-Moreau, D.W.,Chatterjee, K.,Rosenberg, D.J.,Batyuk, A.,Gee, L.B.,Alonso-Mori, R.,Sauter, N.K.,Yano, J.,Yachandra, V.K.,John, J.,Aurelius, O.,Brewster, A.S.,Kern, J.F.,Blomberg, B.,Lebrette, H.,Xu, H.,Hofer, G.,Hogbom, M.,Zou, X.
Tracking the redox reaction of the iron enzyme ribonucleotide reductase using continuous SerialED and SFX.
Structure, 2026

PubMed Abstract: 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-Fe), reduced (Fe-Fe), and re-oxidized states at ∼1.8 Å 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.

PubMed: 42097140
DOI: 10.1016/j.str.2026.03.006

Experimental method

X-RAY DIFFRACTION (2.7 Å)