3o2e: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3o2e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Babesia_bovis Babesia bovis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O2E FirstGlance]. <br> | <table><tr><td colspan='2'>[[3o2e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Babesia_bovis Babesia bovis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O2E FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>< | </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=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k9g|3k9g]], [[3km3|3km3]], [[3kw3|3kw3]], [[3luz|3luz]], [[3men|3men]], [[3njb|3njb]], [[3oib|3oib]], [[3p96|3p96]], [[3pfd|3pfd]], [[3pm6|3pm6]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k9g|3k9g]], [[3km3|3km3]], [[3kw3|3kw3]], [[3luz|3luz]], [[3men|3men]], [[3njb|3njb]], [[3oib|3oib]], [[3p96|3p96]], [[3pfd|3pfd]], [[3pm6|3pm6]]</td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GeneID:5478071 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5865 Babesia bovis])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GeneID:5478071 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5865 Babesia bovis])</td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o2e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o2e RCSB], [http://www.ebi.ac.uk/pdbsum/3o2e PDBsum]</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=3o2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o2e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o2e RCSB], [http://www.ebi.ac.uk/pdbsum/3o2e PDBsum]</span></td></tr> | ||
<table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836<ref>PMID:21359836</ref> | SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836<ref>PMID:21359836</ref> | ||
From | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
== References == | == References == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Babesia bovis]] | [[Category: Babesia bovis]] | ||
[[Category: | [[Category: Structural genomic]] | ||
[[Category: Babesia bovi]] | [[Category: Babesia bovi]] | ||
[[Category: Bol like protein]] | [[Category: Bol like protein]] | ||
[[Category: Iodide]] | [[Category: Iodide]] | ||
[[Category: Sad]] | [[Category: Sad]] | ||
[[Category: Ssgcid]] | [[Category: Ssgcid]] | ||
[[Category: Unknown function]] | [[Category: Unknown function]] | ||
Revision as of 06:01, 25 December 2014
Crystal structure of a bol-like protein from babesia bovisCrystal structure of a bol-like protein from babesia bovis
Structural highlights
Publication Abstract from PubMedThe Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment. SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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