2c2f - Revision history

OCA at 08:25, 9 April 2025

2025-04-09T08:25:16Z

← Older revision		Revision as of 08:25, 9 April 2025
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/2c2f_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/2c2f_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 11:25, 22 May 2024

2024-05-22T11:25:14Z

← Older revision		Revision as of 11:25, 22 May 2024
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	<StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Deira Deira~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2f]] is a 1 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=2C2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.61Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2c2u\|2c2u]]</div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [https://pdbe.org/2c2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [https://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f ProSAT]</span></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=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [https://pdbe.org/2c2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [https://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA]] 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). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref>		[https://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA] 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). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Deira~~]]		[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: McSweeney, S]]		[[Category: McSweeney S]]
	[[Category: Mitchell, E]]		[[Category: Mitchell E]]
	[[Category: Romao~~, C V]]~~		[[Category: Romao CV]]
	~~[[Category: Deinococcus radioduran]]~~
	~~[[Category: Dna binding protein]]~~
	~~[[Category: Dna-binding protein]]~~
	~~[[Category: Dp]]~~
	~~[[Category: Iron~~]]

OCA at 06:46, 1 December 2021

2021-12-01T06:46:45Z

← Older revision		Revision as of 06:46, 1 December 2021
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	<StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2C2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2c2u\|2c2u]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [~~http~~://pdbe.org/2c2f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f ProSAT]</span></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=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [https://pdbe.org/2c2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [https://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA]] 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). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref>		[[https://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA]] 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). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2c2f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2c2f" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Ferritin 3D structures\|Ferritin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:07, 26 February 2020

2020-02-26T11:07:52Z

← Older revision		Revision as of 11:07, 26 February 2020
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	==Dps from Deinococcus radiodurans==		==Dps from Deinococcus radiodurans==
	<StructureSection load='2c2f' size='340' side='right' caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Deira]]		[[Category: Deira]]
			[[Category: Large Structures]]
	[[Category: McSweeney, S]]		[[Category: McSweeney, S]]
	[[Category: Mitchell, E]]		[[Category: Mitchell, E]]

OCA at 08:36, 23 May 2018

2018-05-23T08:36:37Z

← Older revision		Revision as of 08:36, 23 May 2018
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	==~~DPS FROM DEINOCOCCUS RADIODURANS~~==
			==Dps from Deinococcus radiodurans==
	<StructureSection load='2c2f' size='340' side='right' caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='2c2f' size='340' side='right' caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://pdbe.org/2c2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://pdbe.org/2c2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/2c2f_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/2c2f_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</StructureSection>		</StructureSection>
	[[Category: Deira]]		[[Category: Deira]]
	[[Category: ~~Mcsweeney~~, S]]		[[Category: McSweeney, S]]
	[[Category: Mitchell, E]]		[[Category: Mitchell, E]]
	[[Category: Romao, C V]]		[[Category: Romao, C V]]
	[[Category: Deinococcus radioduran]]		[[Category: Deinococcus radioduran]]
			[[Category: Dna binding protein]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Dp]]		[[Category: Dp]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 22:20, 8 February 2016

2016-02-08T22:20:29Z

← Older revision		Revision as of 22:20, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</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=2c2f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:54, 10 September 2015

2015-09-10T15:54:34Z

← Older revision		Revision as of 15:54, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2c2f' size='340' side='right' caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='2c2f' size='340' side='right' caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Deinococcus_radiodurans Deinococcus radiodurans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://pdbe.org/2c2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA]] 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). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2c2f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Deinococcus radiodurans~~]]		[[Category: Deira]]
	[[Category: Mcsweeney, S]]		[[Category: Mcsweeney, S]]
	[[Category: Mitchell, E]]		[[Category: Mitchell, E]]

OCA at 18:23, 15 January 2015

2015-01-15T18:23:11Z

← Older revision		Revision as of 18:23, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Mcsweeney, S.]]		[[Category: Mcsweeney, S]]
	[[Category: Mitchell, E.]]		[[Category: Mitchell, E]]
	[[Category: Romao, C V.]]		[[Category: Romao, C V]]
	[[Category: Deinococcus radioduran]]		[[Category: Deinococcus radioduran]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Dp]]		[[Category: Dp]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 02:57, 30 September 2014

2014-09-30T02:57:00Z

← Older revision		Revision as of 02:57, 30 September 2014
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	[[Image:~~2c2f~~.~~png~~\|~~left~~\|~~200px~~]]		==DPS FROM DEINOCOCCUS RADIODURANS==
			<StructureSection load='2c2f' size='340' side='right' caption='[[2c2f]], [[Resolution\|resolution]] 1.61Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c2u\|2c2u]]</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum]</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/c2/2c2f_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/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The crystal structure of a DNA-binding protein from starved cells (Dps) (DR2263) from Deinococcus radiodurans was determined in two states: a native form, to 1.1-A resolution, and one soaked in an iron solution, to 1.6-A resolution. In comparison with other Dps proteins, DR2263 has an extended N-terminal extension, in both structures presented here, a novel metal binding site was identified in this N-terminal extension and was assigned to bound zinc. The zinc is tetrahedrally coordinated and the ligands, that belong to the N-terminal extension, are two histidines, one glutamate and one aspartate residue, which are unique to this protein within the Dps family. In the iron-soaked crystal structure, a total of three iron sites per monomer were found: one site corresponds to the ferroxidase centre with structural similarities to those found in other Dps family members; the two other sites are located on the two different threefold axes corresponding to small pores in the Dps sphere, which may possibly form the entrance and exit channels for iron storage.

	~~{{STRUCTURE_2c2f\| PDB=2c2f \| SCENE= }}~~		The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus.,Romao CV, Mitchell EP, McSweeney S J Biol Inorg Chem. 2006 Oct;11(7):891-902. Epub 2006 Jul 20. PMID:16855817<ref>PMID:16855817</ref>

	~~===DPS FROM DEINOCOCCUS RADIODURANS===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16855817}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2c2f]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016855817<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Mcsweeney, S.]]		[[Category: Mcsweeney, S.]]

OCA: Protected "2c2f" [edit=sysop:move=sysop]

2013-01-06T12:07:11Z

Protected "2c2f" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:07, 6 January 2013
(No difference)