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New page: left|200px<br /> <applet load="1w3m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1w3m, resolution 1.00Å" /> '''CRYSTAL STRUCTURE O...
 
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[[Image:1w3m.gif|left|200px]]<br />
<applet load="1w3m" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1w3m, resolution 1.00&Aring;" />
'''CRYSTAL STRUCTURE OF TSUSHIMYCIN'''<br />


==Overview==
==Crystal structure of tsushimycin==
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, ... [[http://ispc.weizmann.ac.il/pmbin/getpm?16041082 (full description)]]
<StructureSection load='1w3m' size='340' side='right'caption='[[1w3m]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
== Structural highlights ==
<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>
</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&#8491;</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 ==
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.


==About this Structure==
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>
1W3M is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Actinoplanes_friuliensis Actinoplanes friuliensis]] with CA, CL and EOH as [[http://en.wikipedia.org/wiki/ligands ligands]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W3M OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16041082 16041082]
</div>
<div class="pdbe-citations 1w3m" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Actinoplanes friuliensis]]
[[Category: Actinoplanes friuliensis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bunkoczi, G.]]
[[Category: Bunkoczi G]]
[[Category: Sheldrick, G.M.]]
[[Category: Sheldrick GM]]
[[Category: Vertesy, L.]]
[[Category: Vertesy L]]
[[Category: CA]]
[[Category: CL]]
[[Category: EOH]]
[[Category: amphomycin]]
[[Category: antibiotic]]
[[Category: daptomycin]]
[[Category: lipopetide]]
 
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