9z34 | pdb_00009z34

RT XFEL structure of one-flash state of Photosystem II (1F, S2 rich) at 1.98 Angstrom obtained from anomalous data at 9.5 keV

spinqualitylabelsall models 9z34, resolution 1.98Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9z34 is a 20 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.98Å Ligands: BCR, BCT, CL, CLA, DGD, FE2, FME, HEC, HEM, LHG, LMG, OEX, PHO, PL9, SQD, STE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed During photosynthetic water oxidation, the Mn(4)Ca cluster in Photosystem II progresses through five intermediate S(i) (i = 0-4) states. X-ray crystallography studies have reported the insertion of one new O ligand during the formation of the S(3) state, but recent studies question the presence of this additional ligand based on cryo-EM and earlier room-temperature crystallography data. There is also controversy about whether the O-O bond interaction already occurs in the S(3) state or in the subsequent S(3) to S(0) transition. Here we report conventional high-resolution data for the S(1), S(2), and S(3) states to a resolution of ~1.9 A, and anomalous diffraction data at two energies (9.5 keV and 7 keV), that was used to model the Mn positions, followed by determination of oxygen positions using the high-resolution maps. We show that the new oxygen atom, O(X) (or O6), in the S(3) state is observable as a distinct peak without any restraints, confirming its ligation to Mn1 and Ca. The O(X)-O5 distance is ~2.1 A, supporting no strong interaction between them in the S(3) state, suggesting that if this is the O-O bond formation site, it is formed during the S(3) to S(0) transition initiated by the final oxidation of the cluster. An additional water is introduced into the manganese cluster during the formation of the S(3) state of photosystem II.,Bhowmick A, Zhang M, Simon PS, Makita H, Nangca II, Szilagyi E, Kretzschmar M, Doyle MD, Minnetian NM, Hussein R, Hart O, Chatterjee K, Aydin AO, Shevela D, Cheah MH, Croy N, Chernev P, Fransson T, Tiwari V, Sanchez H, Schleissner P, Lemons R, Gate G, Henstridge M, Glownia JM, Poitevin F, Rosenberg DJ, Dehe S, Gee LB, Tono K, Owada S, Oggenfuss R, Ozerov D, Sander M, Mankowsky R, Lemke HT, Young ID, Holton JM, Mittan-Moreau DW, Paley DW, Afonine PV, Moriarty NW, Adams PD, Mamedov F, Dobbek H, Zouni A, Alonso-Mori R, Bergmann U, Brewster AS, Sauter NK, Messinger J, Kern JF, Yachandra VK, Yano J Nat Commun. 2026 Aug 22;17(1):8818. doi: 10.1038/s41467-026-76805-9. PMID:42632826 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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