9z34: Difference between revisions

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'''Unreleased structure'''


The entry 9z34 is ON HOLD  until Paper Publication
==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==
<StructureSection load='9z34' size='340' side='right'caption='[[9z34]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9z34]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9Z34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Z34 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9z34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9z34 OCA], [https://pdbe.org/9z34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9z34 RCSB], [https://www.ebi.ac.uk/pdbsum/9z34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9z34 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== 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.


Authors:  
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<ref>PMID:42632826</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 9z34" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermosynechococcus vestitus BP-1]]
[[Category: Bhowmick A]]
[[Category: Kern J]]
[[Category: Minnetian NM]]
[[Category: Yachandra VK]]
[[Category: Yano J]]
[[Category: Zhang M]]
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