6ard
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 6ard is ON HOLD Authors: Thompson, M.C., Cascio, D., Yeates, T.O. Description: Monoclinic EutL -structure determined from merged ""Group 2"" data [...) |
|||
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Monoclinic EutL - structure determined from merged "Group 2" data== | |
| + | <StructureSection load='6ard' size='340' side='right'caption='[[6ard]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6ard]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ARD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ARD 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]] 2Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=6ard FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ard OCA], [https://pdbe.org/6ard PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ard RCSB], [https://www.ebi.ac.uk/pdbsum/6ard PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ard ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/EUTL_CLOPE EUTL_CLOPE] A component of the bacterial microcompartment (BMC) shell dedicated to ethanolamine degradation. May be involved in cofactor diffusion across the BMC (Probable). Cobalamin is covalently bound to 1 subunit of the trimer on the concave (lumenal) face in a closed pore conformation; whether this is physiologically relevant is unclear (PubMed:25484204). The closed form has 3 very narrow channels (1.3 Angstrom at their narrowest) per trimer lined by acidic and aromatic residues; 2 ethanolamine molecules can bind in each channel, on either side of the constriction. Does not bind acetate, ethanol or acetyl phosphate, all of which are small molecules involved in ethanolamine metabolism (PubMed:25752492). Ethanolamine-binding has been hypothesized to stabilize the EutL central pore in a closed (non-transporting) state. An open pore is thought to be large enough to transport ATP and/or cobalamin (Probable).<ref>PMID:25484204</ref> <ref>PMID:25752492</ref> <ref>PMID:25484204</ref> <ref>PMID:25752492</ref> <ref>PMID:29717712</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments. | ||
| - | + | Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism.,Thompson MC, Cascio D, Yeates TO Acta Crystallogr D Struct Biol. 2018 May 1;74(Pt 5):411-421. doi:, 10.1107/S2059798318003479. Epub 2018 Apr 24. PMID:29717712<ref>PMID:29717712</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6ard" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Clostridium perfringens]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Cascio D]] | ||
| + | [[Category: Thompson MC]] | ||
| + | [[Category: Yeates TO]] | ||
Current revision
Monoclinic EutL - structure determined from merged "Group 2" data
| |||||||||||
