3lmb: Difference between revisions

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[[Image:3lmb.png|left|200px]]


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==The crystal structure of the protein OLEI01261 with unknown function from Chlorobaculum tepidum TLS==
The line below this paragraph, containing "STRUCTURE_3lmb", creates the "Structure Box" on the page.
<StructureSection load='3lmb' size='340' side='right'caption='[[3lmb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3lmb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oleispira_antarctica_RB-8 Oleispira antarctica RB-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LMB FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_3lmb|  PDB=3lmb  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3lmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lmb OCA], [https://pdbe.org/3lmb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lmb RCSB], [https://www.ebi.ac.uk/pdbsum/3lmb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lmb ProSAT]</span></td></tr>
</table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lm/3lmb_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <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=3lmb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis-the paradigm of mesophilic hydrocarbonoclastic bacteria-O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.


===The crystal structure of the protein OLEI01261 with unknown function from Chlorobaculum tepidum TLS===
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.,Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni ME, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lunsdorf H, Fernandez M, Juarez S, Ciordia S, Singer A, Kagan O, Egorova O, Alain Petit P, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martinez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN Nat Commun. 2013 Jul 23;4:2156. doi: 10.1038/ncomms3156. PMID:23877221<ref>PMID:23877221</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
[[3lmb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LMB OCA].
<div class="pdbe-citations 3lmb" style="background-color:#fffaf0;"></div>
[[Category: Bacteria]]
== References ==
[[Category: Edwards, A.]]
<references/>
[[Category: Egorova, O.]]
__TOC__
[[Category: Evdokimova, E.]]
</StructureSection>
[[Category: Joachimiak, A.]]
[[Category: Large Structures]]
[[Category: MCSG, Midwest Center for Structural Genomics.]]
[[Category: Oleispira antarctica RB-8]]
[[Category: Savchenko, A.]]
[[Category: Edwards A]]
[[Category: Zhang, R.]]
[[Category: Egorova O]]
[[Category: Chlorobaculum tepidum tl]]
[[Category: Evdokimova E]]
[[Category: Mcsg]]
[[Category: Joachimiak A]]
[[Category: Midwest center for structural genomic]]
[[Category: Savchenko A]]
[[Category: Protein olei01261]]
[[Category: Zhang R]]
[[Category: Protein structure initiative]]
[[Category: Psi2]]
[[Category: Structural genomic]]
[[Category: Unknown function]]

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