3l5o: Difference between revisions
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==Crystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from Desulfitobacterium hafniense DCB-2 at 2.01 A resolution== | ==Crystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from Desulfitobacterium hafniense DCB-2 at 2.01 A resolution== | ||
<StructureSection load='3l5o' size='340' side='right' caption='[[3l5o]], [[Resolution|resolution]] 2.01Å' scene=''> | <StructureSection load='3l5o' size='340' side='right'caption='[[3l5o]], [[Resolution|resolution]] 2.01Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3l5o]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3l5o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfitobacterium_hafniense_DCB-2 Desulfitobacterium hafniense DCB-2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h1q 2h1q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L5O FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3l5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l5o OCA], [https://pdbe.org/3l5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l5o RCSB], [https://www.ebi.ac.uk/pdbsum/3l5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l5o ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/B8FUJ5_DESHD B8FUJ5_DESHD] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l5/3l5o_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l5/3l5o_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3l5o ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<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 3l5o" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Desulfitobacterium hafniense]] | [[Category: Desulfitobacterium hafniense DCB-2]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Structural genomic]] | [[Category: Structural genomic]] | ||
Latest revision as of 14:44, 1 February 2023
Crystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from Desulfitobacterium hafniense DCB-2 at 2.01 A resolutionCrystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from Desulfitobacterium hafniense DCB-2 at 2.01 A resolution
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 A using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.,Miller MD, Aravind L, Bakolitsa C, Rife CL, Carlton D, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1167-73. Epub 2010 Jul 6. PMID:20944207[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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