9S5R
Time-resolved SFX series of the DtpAa Y389F variant mixed with hydrogen peroxide -time 5 s
Summary for 9S5R
| Entry DOI | 10.2210/pdb9s5r/pdb |
| Descriptor | Deferrochelatase, PROTOPORPHYRIN IX CONTAINING FE, OXYGEN ATOM, ... (4 entities in total) |
| Functional Keywords | peroxidase, compound i, compound ii, dyp, dtpaa, oxidoreductase |
| Biological source | Streptomyces lividans |
| Total number of polymer chains | 2 |
| Total formula weight | 81729.01 |
| Authors | |
| Primary citation | Williams, L.J.,Kamps, J.J.A.G.,Branzanic, A.M.V.,Lehene, M.,Lundgren, K.J.M.,Ryde, U.,Chatterjee, K.,Doyle, M.D.,Simon, P.S.,Makita, H.,Thompson, A.J.,Brewster, A.S.,Zhou, T.,Lucic, M.,Wilson, M.T.,Aller, P.,Sanchez-Weatherby, J.,Gee, L.,Dehe, S.,Mous, S.,Yano, J.,Yachandra, V.K.,Hough, M.A.,Orville, A.M.,Kern, J.F.,Silaghi-Dumitrescu, R.L.,Worrall, J.A.R. Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates? Nat Commun, 17:-, 2026 Cited by PubMed Abstract: The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with HO have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe-OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe-O) character. Such states offer insight into the nature of ferryl heme. PubMed: 41634046DOI: 10.1038/s41467-026-69192-8 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
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