6ye4: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy== | ==Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy== | ||
<StructureSection load='6ye4' size='340' side='right'caption='[[6ye4]]' scene=''> | <StructureSection load='6ye4' size='340' side='right'caption='[[6ye4]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE4 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6ye4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE4 FirstGlance]. <br> | ||
</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=6ye4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye4 OCA], [https://pdbe.org/6ye4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye4 ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGT:(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+STEARATE'>PGT</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">exbB, FG174_21755, PWN146_03792 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889])</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=6ye4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye4 OCA], [https://pdbe.org/6ye4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye4 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs. | |||
RELION: implementation of a Bayesian approach to cryo-EM structure determination.,Scheres SH J Struct Biol. 2012 Dec;180(3):519-30. doi: 10.1016/j.jsb.2012.09.006. Epub 2012 , Sep 19. PMID:23000701<ref>PMID:23000701</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6ye4" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[ExbB|ExbB]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Biou V]] | [[Category: Biou, V]] | ||
[[Category: Chami M]] | [[Category: Chami, M]] | ||
[[Category: Coureux | [[Category: Coureux, P D]] | ||
[[Category: Delepelaire P]] | [[Category: Delepelaire, P]] | ||
[[Category: Iron uptake]] | |||
[[Category: Membrane protein]] | |||
[[Category: Metal transport]] | |||
[[Category: Proton transfer]] | |||
[[Category: Tonb complex]] | |||
Revision as of 15:46, 13 October 2021
Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopyStructure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy
Structural highlights
Publication Abstract from PubMedRELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs. RELION: implementation of a Bayesian approach to cryo-EM structure determination.,Scheres SH J Struct Biol. 2012 Dec;180(3):519-30. doi: 10.1016/j.jsb.2012.09.006. Epub 2012 , Sep 19. PMID:23000701[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||