This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2w6k
From Proteopedia
(Difference between revisions)
m (Protected "2w6k" [edit=sysop:move=sysop]) |
|||
| (5 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2w6k.png|left|200px]] | ||
| - | + | ==The crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway== | |
| + | <StructureSection load='2w6k' size='340' side='right'caption='[[2w6k]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2w6k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2bsn 2bsn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W6K FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2w6l|2w6l]]</div></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=2w6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w6k OCA], [https://pdbe.org/2w6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w6k RCSB], [https://www.ebi.ac.uk/pdbsum/2w6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w6k 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/w6/2w6k_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=2w6k ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | CobE, a protein implicated in vitamin B12 biosynthesis, from Pseudomonas aeruginosa has been overexpressed in Escherichia coli, purified and crystallized using hanging-drop vapour diffusion. The crystals belong to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 31.86, b = 41.07, c = 87.41 A. The diffraction extends to a resolution of 1.9 A. There is one molecule per asymmetric unit and the estimated solvent content is 35%. SeMet-labelled CobE has been prepared and crystallizes under the same conditions as the native protein with diffraction to 1.7 A. The anomalous measurements will be used for phasing. | ||
| - | + | Crystallization and preliminary structure analysis of CobE, an essential protein of cobalamin (vitamin B12) biosynthesis.,Vevodova J, Graham RM, Raux E, Warren MJ, Wilson KS Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Apr 1;61(Pt, 4):442-4. Epub 2005 Apr 1. PMID:16511064<ref>PMID:16511064</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2w6k" style="background-color:#fffaf0;"></div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | == | + | __TOC__ |
| - | < | + | </StructureSection> |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Deery, E | + | [[Category: Deery, E]] |
| - | [[Category: | + | [[Category: McGoldrick, H]] |
| - | [[Category: Murzin, A G | + | [[Category: Murzin, A G]] |
| - | [[Category: Smith, D | + | [[Category: Smith, D]] |
| - | [[Category: Vevodova, J | + | [[Category: Vevodova, J]] |
| - | [[Category: Warren, M J | + | [[Category: Warren, M J]] |
| - | [[Category: Wilson, K S | + | [[Category: Wilson, K S]] |
[[Category: Biosynthetic protein]] | [[Category: Biosynthetic protein]] | ||
[[Category: Cobalamin]] | [[Category: Cobalamin]] | ||
Current revision
The crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway
| |||||||||||
