4tnh: Difference between revisions

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-'''Unreleased structure'''
+==RT XFEL structure of Photosystem II in the dark state at 4.9 A resolution==
+<StructureSection load='4tnh' size='340' side='right' caption='[[4tnh]], [[Resolution|resolution]] 4.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4tnh]] 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=4TNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNH FirstGlance]. <br>
+</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>
+<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4tni|4tni]], [[4tnj|4tnj]], [[4tnk|4tnk]]</td></tr>
+<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>
+<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=4tnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tnh RCSB], [http://www.ebi.ac.uk/pdbsum/4tnh PDBsum]</span></td></tr>
+<table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-The entry 4tnh is ON HOLD
+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>
-Authors: Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G., Gildea, R.J., Han, G., Hellmich, J., Lassalle-Kaiser, B., Chatterjee, R., Brewster, A., Stan, C.A., Gloeckner, C., Lampe, A., DiFiore, D., Milathianaki, D., Fry, A.R., Seibert, M.M., Koglin, J.E., Gallo, E., Uhlig, J., Sokaras, D., Weng, T.-C., Zwart, P.H., Skinner, D.E., Bogan, M.J., Messerschmidt, M., Glatzel, P., Williams, G.J., Boutet, S., Adams, P.D., Zouni, A., Messinger, J., Sauter, N.K., Bergmann, U., Yano, J., Yachandra, V.K.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: RT XFEL structure of Photosystem II in the dark state at 4.9 A resolution
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Photosystem II]]
+[[Category: Thermosynechococcus elongatus]]
+[[Category: Adams, P D.]]
+[[Category: Alonso-Mori, R.]]
+[[Category: Bergmann, U.]]
+[[Category: Bogan, M J.]]
+[[Category: Boutet, S.]]
+[[Category: Brewster, A.]]
+[[Category: Chatterjee, R.]]
+[[Category: DiFiore, D.]]
+[[Category: Echols, N.]]
+[[Category: Fry, A R.]]
+[[Category: Gallo, E.]]
+[[Category: Gildea, R J.]]
+[[Category: Glatzel, P.]]
+[[Category: Gloeckner, C.]]
+[[Category: Gul, S.]]
+[[Category: Han, G.]]
+[[Category: Hattne, J.]]
+[[Category: Hellmich, J.]]
+[[Category: Ibrahim, M.]]
+[[Category: Kern, J.]]
+[[Category: Koglin, J E.]]
+[[Category: Koroidov, S.]]
+[[Category: Laksmono, H.]]
+[[Category: Lampe, A.]]
+[[Category: Lassalle-Kaiser, B.]]
+[[Category: Messerschmidt, M.]]
+[[Category: Messinger, J.]]
+[[Category: Milathianaki, D.]]
+[[Category: Sauter, N K.]]
+[[Category: Seibert, M M.]]
+[[Category: Sierra, R G.]]
+[[Category: Skinner, D E.]]
+[[Category: Sokaras, D.]]
+[[Category: Stan, C A.]]
+[[Category: Tran, R.]]
+[[Category: Uhlig, J.]]
+[[Category: Weng, T C.]]
+[[Category: Williams, G J.]]
+[[Category: Yachandra, V K.]]
+[[Category: Yano, J.]]
+[[Category: Zouni, A.]]
+[[Category: Zwart, P H.]]
+[[Category: Electron transport]]
+[[Category: Membrane protein]]
+[[Category: Photosynthesis]]
+[[Category: Water oxidation]]
+[[Category: X-ray free electron laser]]