3vdi: Difference between revisions

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[[Image:3vdi.png|left|200px]]


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==Structure of the FMO protein from Pelodictyon phaeum==
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<StructureSection load='3vdi' size='340' side='right'caption='[[3vdi]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3vdi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pelodictyon_phaeum Pelodictyon phaeum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VDI FirstGlance]. <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]] 1.99&#8491;</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=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
{{STRUCTURE_3vdi|  PDB=3vdi  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdi OCA], [https://pdbe.org/3vdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdi RCSB], [https://www.ebi.ac.uk/pdbsum/3vdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdi ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Fenna-Matthews-Olson antenna protein from the green bacterium Pelodictyon phaeum mediates the energy transfer from a peripheral antenna complex to the membrane-bound reaction center. The three-dimensional structure of this protein has been previously modeled using X-ray diffraction to a resolution limit of 2.0 A, with R (work) and R (free) values of 16.6 and 19.9 %, respectively (Larson et al., Photosynth Res 107:139-150, 2011). This model shows the protein as consisting of beta-sheets surrounding several bacteriochlorophyll cofactors. While most of the model clearly matches the electron density maps, in this paper we re-examine the electron density for a specific feature, namely the eighth bacteriochlorophyll a cofactor. This electron density is now interpreted as arising primarily from the end of an otherwise disordered polyethylene glycol molecule. Additional electron density is present but the density is weak and cannot be unambiguously assigned. The new model has R (work) and R (free) values of 16.2 and 19.0 %, respectively.


===Structure of the FMO protein from Pelodictyon phaeum===
Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum.,Tronrud DE, Allen JP Photosynth Res. 2012 Mar 29. PMID:22457093<ref>PMID:22457093</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
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{{ABSTRACT_PUBMED_22457093}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3vdi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pelodictyon_phaeum Pelodictyon phaeum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3oeg 3oeg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDI OCA].
 
==Reference==
<ref group="xtra">PMID:022457093</ref><ref group="xtra">PMID:021181557</ref><references group="xtra"/>
[[Category: Pelodictyon phaeum]]
[[Category: Pelodictyon phaeum]]
[[Category: Allen, J P.]]
[[Category: Allen JP]]
[[Category: Blankenship, R E.]]
[[Category: Blankenship RE]]
[[Category: Larson, C R.]]
[[Category: Larson CR]]
[[Category: Lauman, L.]]
[[Category: Lauman L]]
[[Category: Matthies, H J.]]
[[Category: Matthies HJ]]
[[Category: Seng, C O.]]
[[Category: Seng CO]]
[[Category: Tronrud, D E.]]
[[Category: Tronrud DE]]
[[Category: Wen, J.]]
[[Category: Wen J]]
[[Category: Alpha/beta protein]]
[[Category: Energy transfer]]
[[Category: Photosynthesis]]
Retrieved from "https://proteopedia.org/3vdi"