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.
2cdy
From Proteopedia
(Difference between revisions)
| (21 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2cdy.gif|left|200px]]<br /> | ||
| - | <applet load="2cdy" size="450" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2cdy, resolution 2.00Å" /> | ||
| - | '''MANGANESE SUPEROXIDE DISMUTASE (MN-SOD) FROM DEINOCOCCUS RADIODURANS'''<br /> | ||
| - | == | + | ==Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans== |
| - | The structure of the manganese superoxide dismutase (Mn-SOD; DR1279) from | + | <StructureSection load='2cdy' size='340' side='right'caption='[[2cdy]], [[Resolution|resolution]] 2.00Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2cdy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CDY FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2cdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cdy OCA], [https://pdbe.org/2cdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cdy RCSB], [https://www.ebi.ac.uk/pdbsum/2cdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cdy ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/SODM_DEIRA SODM_DEIRA] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems (By similarity). | ||
| + | == 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/cd/2cdy_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=2cdy ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The structure of the manganese superoxide dismutase (Mn-SOD; DR1279) from Deinococcus radiodurans has been determined in two different crystal forms. Both crystal forms are monoclinic with space group P2(1). Form I has unit-cell parameters a = 44.28, b = 83.21, c = 59.52 angstroms, beta = 110.18 degrees and contains a homodimer in the asymmetric unit, with structure refinement (R = 16.8%, R(free) = 23.6%) carried out using data to d(min) = 2.2 angstroms. Form II has unit-cell parameters a = 43.57, b = 87.10, c = 116.42 angstroms, beta = 92.1 degrees and an asymmetric unit containing two Mn-SOD homodimers; structure refinement was effected to a resolution of 2.0 angstroms (R = 17.2%, R(free) = 22.3%). The resulting structures are compared with that of Mn-SOD from Escherichia coli, with which they are shown to be essentially isostructural. | ||
| - | + | Structure of the manganese superoxide dismutase from Deinococcus radiodurans in two crystal forms.,Dennis RJ, Micossi E, McCarthy J, Moe E, Gordon EJ, Kozielski-Stuhrmann S, Leonard GA, McSweeney S Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt, 4):325-9. Epub 2006 Mar 25. PMID:16582477<ref>PMID:16582477</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2cdy" style="background-color:#fffaf0;"></div> | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ==See Also== | |
| + | *[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Deinococcus radiodurans R1]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Dennis R]] | ||
| + | [[Category: Gordon E]] | ||
| + | [[Category: Leonard G]] | ||
| + | [[Category: McCarthy J]] | ||
| + | [[Category: McSweeney S]] | ||
| + | [[Category: Micossi E]] | ||
| + | [[Category: Moe E]] | ||
Current revision
Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans
| |||||||||||
