4tnk

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==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==
==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==
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<StructureSection load='4tnk' size='340' side='right' caption='[[4tnk]], [[Resolution|resolution]] 5.20&Aring;' scene=''>
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<StructureSection load='4tnk' size='340' side='right'caption='[[4tnk]], [[Resolution|resolution]] 5.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4tnk]] 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=4TNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=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=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</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><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 5.2&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
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<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=CA:CALCIUM+ION'>CA</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=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=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</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></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4tnh|4tnh]], [[4tni|4tni]], [[4tnj|4tnj]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [https://pdbe.org/4tnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [https://www.ebi.ac.uk/pdbsum/4tnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnk ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>
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</table>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>
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== Function ==
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<table>
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[https://www.uniprot.org/uniprot/PSBA1_THEVB PSBA1_THEVB] Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
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The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 mus after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 mus after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 A. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.
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Towards automated crystallographic structure refinement with phenix.refine.,Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi:, 10.1107/S0907444912001308. Epub 2012 Mar 16. PMID:22505256<ref>PMID:22505256</ref>
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Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.,Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glockner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371. PMID:25006873<ref>PMID:25006873</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
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<div class="pdbe-citations 4tnk" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
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*[[Photosystem II 3D structures|Photosystem II 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Photosystem II]]
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[[Category: Large Structures]]
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[[Category: Thermosynechococcus elongatus]]
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[[Category: Thermosynechococcus vestitus BP-1]]
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[[Category: Adams, P D.]]
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[[Category: Adams PD]]
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[[Category: Alonso-Mori, R.]]
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[[Category: Alonso-Mori R]]
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[[Category: Bergmann, U.]]
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[[Category: Bergmann U]]
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[[Category: Bogan, M J.]]
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[[Category: Bogan MJ]]
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[[Category: Boutet, S.]]
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[[Category: Boutet S]]
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[[Category: Brewster, A.]]
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[[Category: Brewster A]]
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[[Category: Chatterjee, R.]]
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[[Category: Chatterjee R]]
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[[Category: DiFiore, D.]]
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[[Category: DiFiore D]]
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[[Category: Echols, N.]]
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[[Category: Echols N]]
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[[Category: Fry, A R.]]
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[[Category: Fry AR]]
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[[Category: Gallo, E.]]
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[[Category: Gallo E]]
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[[Category: Gildea, R J.]]
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[[Category: Gildea RJ]]
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[[Category: Glatzel, P.]]
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[[Category: Glatzel P]]
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[[Category: Gloeckner, C.]]
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[[Category: Gloeckner C]]
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[[Category: Gul, S.]]
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[[Category: Gul S]]
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[[Category: Han, G.]]
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[[Category: Han G]]
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[[Category: Hattne, J.]]
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[[Category: Hattne J]]
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[[Category: Hellmich, J.]]
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[[Category: Hellmich J]]
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[[Category: Ibrahim, M.]]
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[[Category: Ibrahim M]]
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[[Category: Kern, J.]]
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[[Category: Kern J]]
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[[Category: Koglin, J E.]]
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[[Category: Koglin JE]]
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[[Category: Koroidov, S.]]
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[[Category: Koroidov S]]
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[[Category: Laksmono, H.]]
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[[Category: Laksmono H]]
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[[Category: Lampe, A.]]
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[[Category: Lampe A]]
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[[Category: Lassalle-Kaiser, B.]]
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[[Category: Lassalle-Kaiser B]]
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[[Category: Messerschmidt, M.]]
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[[Category: Messerschmidt M]]
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[[Category: Messinger, J.]]
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[[Category: Messinger J]]
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[[Category: Milathianaki, D.]]
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[[Category: Milathianaki D]]
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[[Category: Sauter, N K.]]
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[[Category: Sauter NK]]
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[[Category: Seibert, M M.]]
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[[Category: Seibert MM]]
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[[Category: Sierra, R G.]]
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[[Category: Sierra RG]]
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[[Category: Skinner, D E.]]
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[[Category: Skinner DE]]
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[[Category: Sokaras, D.]]
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[[Category: Sokaras D]]
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[[Category: Stan, C A.]]
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[[Category: Stan CA]]
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[[Category: Tran, R.]]
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[[Category: Tran R]]
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[[Category: Uhlig, J.]]
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[[Category: Uhlig J]]
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[[Category: Weng, T C.]]
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[[Category: Weng T-C]]
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[[Category: Williams, G J.]]
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[[Category: Williams GJ]]
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[[Category: Yachandra, V K.]]
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[[Category: Yachandra VK]]
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[[Category: Yano, J.]]
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[[Category: Yano J]]
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[[Category: Zouni, A.]]
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[[Category: Zouni A]]
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[[Category: Zwart, P H.]]
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[[Category: Zwart PH]]
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[[Category: Electron transport]]
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[[Category: Membrane protein]]
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[[Category: Photosynthesis]]
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[[Category: Water oxidation]]
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[[Category: X-ray free electron laser]]
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Current revision

RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution

PDB ID 4tnk

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