3d9b: Difference between revisions

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{{Seed}}
[[Image:3d9b.png|left|200px]]


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==Symmetric structure of E. coli AcrB==
The line below this paragraph, containing "STRUCTURE_3d9b", creates the "Structure Box" on the page.
<StructureSection load='3d9b' size='340' side='right'caption='[[3d9b]], [[Resolution|resolution]] 3.42&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'>[[3d9b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D9B 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]] 3.42&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
{{STRUCTURE_3d9b|  PDB=3d9b  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d9b OCA], [https://pdbe.org/3d9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d9b RCSB], [https://www.ebi.ac.uk/pdbsum/3d9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d9b ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>
== 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/d9/3d9b_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3d9b ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In the course of a crystallographic study of the Methanosarcina mazei CorA transporter, the membrane protein was obtained with at least 95% purity and was submitted to crystallization trials. Small crystals (&lt;100 microm) were grown that diffracted to 3.42 A resolution and belonged to space group R32, with unit-cell parameters a = b = 145.74, c = 514.0 A. After molecular-replacement attempts using available CorA structures as search models failed to yield a solution, it was discovered that the crystals consisted of an Escherichia coli contaminating protein, acriflavine resistance protein B (AcrB), that was present at less than 5% in the protein preparations. AcrB contamination is a major problem when expressing membrane proteins in E. coli since it binds naturally to immobilized metal-ion affinity chromatography (IMAC) resins. Here, the structure is compared with previously deposited AcrB structures and strategies are proposed to avoid this contamination.


===Symmetric structure of E. coli AcrB===
There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization.,Veesler D, Blangy S, Cambillau C, Sciara G Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Oct 1;64(Pt 10):880-5., Epub 2008 Sep 30. PMID:18931428<ref>PMID:18931428</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3D9B is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D9B OCA].
<div class="pdbe-citations 3d9b" style="background-color:#fffaf0;"></div>
[[Category: Bacteria]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Blangy, S.]]
__TOC__
[[Category: Cambillau, C.]]
</StructureSection>
[[Category: Sciara, G.]]
[[Category: Large Structures]]
[[Category: Veesler, D.]]
[[Category: Blangy S]]
[[Category: Alpha-helice]]
[[Category: Cambillau C]]
[[Category: Inner membrane]]
[[Category: Sciara G]]
[[Category: Transmembrane protein]]
[[Category: Veesler D]]
[[Category: Transport]]
[[Category: Transport protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 12:51:27 2008''

Latest revision as of 12:43, 30 August 2023

Symmetric structure of E. coli AcrB

3d9b, resolution 3.42Å

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