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| | ==Gramicidin D complex with sodium iodide== | | ==Gramicidin D complex with sodium iodide== |
| - | <StructureSection load='3l8l' size='340' side='right' caption='[[3l8l]], [[Resolution|resolution]] 1.25Å' scene=''> | + | <StructureSection load='3l8l' size='340' side='right'caption='[[3l8l]], [[Resolution|resolution]] 1.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3l8l]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L8L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3l8l]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L8L FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLE:D-LEUCINE'>DLE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FVA:N-FORMYL-L-VALINE'>FVA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DLE:D-LEUCINE'>DLE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FVA:N-FORMYL-L-VALINE'>FVA</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_000152:GRAMICIDIN+D'>PRD_000152</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tk2|1tk2]], [[2xdc|2xdc]], [[1av2|1av2]], [[1bdw|1bdw]], [[1c4d|1c4d]], [[1gmk|1gmk]], [[1grm|1grm]], [[1jno|1jno]], [[1kqe|1kqe]], [[1mag|1mag]], [[1mic|1mic]], [[1ng8|1ng8]], [[1nrm|1nrm]], [[1nru|1nru]], [[1nt5|1nt5]], [[1jo3|1jo3]], [[1jo4|1jo4]], [[1nt6|1nt6]], [[1tkq|1tkq]], [[1w5u|1w5u]], [[2izq|2izq]], [[1al4|1al4]], [[1alx|1alx]], [[1alz|1alz]]</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=3l8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l8l OCA], [https://pdbe.org/3l8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l8l RCSB], [https://www.ebi.ac.uk/pdbsum/3l8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l8l ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3l8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l8l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l8l RCSB], [http://www.ebi.ac.uk/pdbsum/3l8l PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3l8l" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Brevibacillus brevis]] | | [[Category: Brevibacillus brevis]] |
| - | [[Category: Bojarska, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Duax, W L]] | + | [[Category: Bojarska J]] |
| - | [[Category: Glowka, M L]] | + | [[Category: Duax WL]] |
| - | [[Category: Olczak, A]] | + | [[Category: Glowka ML]] |
| - | [[Category: Szczesio, M]] | + | [[Category: Olczak A]] |
| - | [[Category: Wawrzak, Z]] | + | [[Category: Szczesio M]] |
| - | [[Category: Antibacterial]]
| + | [[Category: Wawrzak Z]] |
| - | [[Category: Antibiotic]]
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| - | [[Category: Antifungal]]
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| - | [[Category: Gramicidin]]
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| - | [[Category: Gramicidin-nai complex]]
| + | |
| - | [[Category: Linear gramicidin]]
| + | |
| - | [[Category: Membrane ion channel]]
| + | |
| Structural highlights
3l8l is a 4 chain structure with sequence from Brevibacillus brevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.25Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
The crystal structure of the nonstoichiometric complex of gramicidin D with NaI has been studied using synchrotron radiation at 100 K. The limiting resolution was 1.25 A and the R factor was 16% for 19 883 observed reflections. The general architecture of the antiparallel two-stranded gramicidin dimers in the studied crystal was a right-handed antiparallel double-stranded form that closely resembles the structures of other right-handed species published to date. However, there were several surprising observations. In addition to the significantly different composition of linear gramicidins identified in the crystal structure, including the absence of the gramicidin C form, only two cationic sites were found in each of the two independent dimers (channels), which were partially occupied by sodium, compared with the seven sites found in the RbCl complex of gramicidin. The sum of the partial occupancies of Na(+) was only 1.26 per two dimers and was confirmed by the similar content of iodine ions (1.21 ions distributed over seven sites), which was easily visible from their anomalous signal. Another surprising observation was the significant asymmetry of the distributions and occupancies of cations in the gramicidin dimers, which was in contrast to those observed in the high-resolution structures of the complexes of heavier alkali metals with gramicidin D, especially that of rubidium.
The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex.,Olczak A, Glowka ML, Szczesio M, Bojarska J, Wawrzak Z, Duax WL Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):874-80. Epub 2010, Jul 9. PMID:20693686[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Olczak A, Glowka ML, Szczesio M, Bojarska J, Wawrzak Z, Duax WL. The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex. Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):874-80. Epub 2010, Jul 9. PMID:20693686 doi:10.1107/S0907444910019876
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