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.
1vel
From Proteopedia
(Difference between revisions)
| (9 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:1vel.png|left|200px]] | ||
| - | + | ==Mycobacterium smegmatis Dps tetragonal form== | |
| - | + | <StructureSection load='1vel' size='340' side='right'caption='[[1vel]], [[Resolution|resolution]] 2.99Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[1vel]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEL 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]] 2.99Å</td></tr> | |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1vel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vel OCA], [https://pdbe.org/1vel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vel RCSB], [https://www.ebi.ac.uk/pdbsum/1vel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vel ProSAT]</span></td></tr> |
| - | [[1vel]] is a 6 chain structure | + | </table> |
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DPS_MYCSM DPS_MYCSM] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). It protects DNA from hydroxyl radical-mediated cleavage. Binds DNA with no apparent sequence specificity without self-aggregation nor promotion of DNA condensation. Is unable to protect DNA from DNase-mediated cleavage.<ref>PMID:12466274</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/ve/1vel_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=1vel ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[Ferritin|Ferritin]] | + | *[[Ferritin 3D structures|Ferritin 3D structures]] |
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| - | [[Category: | + | </StructureSection> |
| - | [[Category: Chatterji | + | [[Category: Large Structures]] |
| - | [[Category: Das | + | [[Category: Mycolicibacterium smegmatis]] |
| - | [[Category: Gupta | + | [[Category: Chatterji D]] |
| - | [[Category: Roy | + | [[Category: Das S]] |
| - | [[Category: Sekar | + | [[Category: Gupta S]] |
| - | [[Category: Vijayan | + | [[Category: Roy S]] |
| - | + | [[Category: Sekar K]] | |
| - | + | [[Category: Vijayan M]] | |
Current revision
Mycobacterium smegmatis Dps tetragonal form
| |||||||||||
