1w3m
From Proteopedia
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==Crystal structure of tsushimycin== | ==Crystal structure of tsushimycin== | ||
| - | <StructureSection load='1w3m' size='340' side='right' caption='[[1w3m]], [[Resolution|resolution]] 1.00Å' scene=''> | + | <StructureSection load='1w3m' size='340' side='right'caption='[[1w3m]], [[Resolution|resolution]] 1.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | [[1w3m]] is a 12 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1w3m]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinoplanes_friuliensis Actinoplanes friuliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W3M FirstGlance]. <br> |
| - | <b> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2AS:(2S,3S)-3-METHYL-ASPARTIC+ACID'>2AS</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPI:6-CARBOXYPIPERIDINE'>CPI</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=LNG:DELTA-3ISOTETRADECENOIC+ACID'>LNG</scene>, <scene name='pdbligand=PRD_000487:Tsushimycin'>PRD_000487</scene>, <scene name='pdbligand=VDL:(2R,3R)-2,3-DIAMINOBUTANOIC+ACID'>VDL</scene>, <scene name='pdbligand=VLL:(2S)-2,3-DIAMINOBUTANOIC+ACID'>VLL</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=1w3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w3m OCA], [https://pdbe.org/1w3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w3m RCSB], [https://www.ebi.ac.uk/pdbsum/1w3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w3m ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding. | The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding. | ||
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Structure of the lipopeptide antibiotic tsushimycin.,Bunkoczi G, Vertesy L, Sheldrick GM Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1160-4. Epub 2005, Jul 20. PMID:16041082<ref>PMID:16041082</ref> | Structure of the lipopeptide antibiotic tsushimycin.,Bunkoczi G, Vertesy L, Sheldrick GM Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1160-4. Epub 2005, Jul 20. PMID:16041082<ref>PMID:16041082</ref> | ||
| - | From | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| + | </div> | ||
| + | <div class="pdbe-citations 1w3m" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Actinoplanes friuliensis]] | [[Category: Actinoplanes friuliensis]] | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Bunkoczi G]] |
| - | [[Category: | + | [[Category: Sheldrick GM]] |
| - | [[Category: | + | [[Category: Vertesy L]] |
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Current revision
Crystal structure of tsushimycin
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