2i6e: Difference between revisions

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[[Image:2i6e.gif|left|200px]]


{{Structure
==Crystal structure of protein DR0370 from Deinococcus radiodurans, Pfam DUF178==
|PDB= 2i6e |SIZE=350|CAPTION= <scene name='initialview01'>2i6e</scene>, resolution 2.50&Aring;
<StructureSection load='2i6e' size='340' side='right'caption='[[2i6e]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I6E FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
|GENE= DR_0370 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 Deinococcus radiodurans])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG1427 COG1427]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2i6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i6e OCA], [https://pdbe.org/2i6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i6e RCSB], [https://www.ebi.ac.uk/pdbsum/2i6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i6e ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2i6e TOPSAN]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2i6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i6e OCA], [http://www.ebi.ac.uk/pdbsum/2i6e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2i6e RCSB]</span>
== Evolutionary Conservation ==
}}
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
'''Crystal structure of protein DR0370 from Deinococcus radiodurans, Pfam DUF178'''
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i6/2i6e_consurf.spt"</scriptWhenChecked>
 
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
==Overview==
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2i6e ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. Pfam has two large series of functionally uncharacterized families, known as Domains of Unknown Function (DUFs) and Uncharacterized Protein Families (UPFs). RESULTS: Crystal structures of two proteins from Deinococcus radiodurans and Streptomyces coelicolor belonging to Pfam protein family DUF178 (ID: PF02621) have been determined using Selenium-Single-wavelength Anomalous Dispersion (Se-SAD). Based on the structure, we have identified the putative function for this family of protein. CONCLUSION: Unexpectedly, we found that DUF178 Pfam is remarkably similar to Pfam family DUF191 suggesting that the sequence-based classification alone may not be sufficient to classify proteins into Pfam families.
BACKGROUND: Pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. Pfam has two large series of functionally uncharacterized families, known as Domains of Unknown Function (DUFs) and Uncharacterized Protein Families (UPFs). RESULTS: Crystal structures of two proteins from Deinococcus radiodurans and Streptomyces coelicolor belonging to Pfam protein family DUF178 (ID: PF02621) have been determined using Selenium-Single-wavelength Anomalous Dispersion (Se-SAD). Based on the structure, we have identified the putative function for this family of protein. CONCLUSION: Unexpectedly, we found that DUF178 Pfam is remarkably similar to Pfam family DUF191 suggesting that the sequence-based classification alone may not be sufficient to classify proteins into Pfam families.


==About this Structure==
X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family.,Tyagi R, Burley SK, Swaminathan S BMC Struct Biol. 2007 Oct 1;7:62. PMID:17908300<ref>PMID:17908300</ref>
2I6E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I6E OCA].
 
==Reference==
X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family., Tyagi R, Burley SK, Swaminathan S, BMC Struct Biol. 2007 Oct 1;7:62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17908300 17908300]
[[Category: Deinococcus radiodurans]]
[[Category: Single protein]]
[[Category: Burley, S K.]]
[[Category: Kumaran, D.]]
[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
[[Category: Swaminathan, S.]]
[[Category: Tyagi, R.]]
[[Category: hypothetical protein,pfam:duf178]]
[[Category: new york structural genomix research consortium]]
[[Category: nysgxrc,10093b]]
[[Category: protein structure initiative]]
[[Category: psi-2]]
[[Category: structural genomic]]
[[Category: unknown function]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:40:22 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2i6e" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Burley SK]]
[[Category: Kumaran D]]
[[Category: Swaminathan S]]
[[Category: Tyagi R]]
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