1tkp - Revision history

OCA at 06:31, 23 August 2023

OCA — Wed, 23 Aug 2023 06:31:45 GMT

←Older revision		Revision as of 06:31, 23 August 2023
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	<StructureSection load='1tkp' size='340' side='right'caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1tkp' size='340' side='right'caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKP 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</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=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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [https://pdbe.org/1tkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [https://www.ebi.ac.uk/pdbsum/1tkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkp 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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [https://pdbe.org/1tkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [https://www.ebi.ac.uk/pdbsum/1tkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPS_HALSA DPS_HALSA]] 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).	+	[https://www.uniprot.org/uniprot/DPS_HALSA DPS_HALSA] 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).
	== 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: ~~Bacillus halobius ruber klebahn 1919~~]]	+	[[Category: Halobacterium salinarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Essen~~, L O~~]]	+	[[Category: Essen LO]]
-	[[Category: Oesterhelt, D]]	+	[[Category: Oesterhelt D]]
-	[[Category: Offermann, S]]	+	[[Category: Offermann S]]
-	[[Category: Zeth, K]]	+	[[Category: Zeth K]]
-	~~[[Category: Dpsa]]~~	+
-	~~[[Category: Ferritin]]~~	+
-	~~[[Category: High iron]]~~	+
-	~~[[Category: Iron cluster]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 09:03, 21 April 2021

OCA — Wed, 21 Apr 2021 09:03:00 GMT

←Older revision		Revision as of 09:03, 21 April 2021
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	<StructureSection load='1tkp' size='340' side='right'caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1tkp' size='340' side='right'caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKP 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [~~http~~://pdbe.org/1tkp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tkp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkp 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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [https://pdbe.org/1tkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [https://www.ebi.ac.uk/pdbsum/1tkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPS_HALSA DPS_HALSA]] 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).	+	[[https://www.uniprot.org/uniprot/DPS_HALSA DPS_HALSA]] 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).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:38, 17 July 2019

OCA — Wed, 17 Jul 2019 13:38:27 GMT

←Older revision		Revision as of 13:38, 17 July 2019
Line 1:		Line 1:

	==Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states==		==Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states==
-	<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1tkp' size='340' side='right'caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tk/1tkp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tk/1tkp_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>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1tkp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1tkp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ferritin 3D structures\|Ferritin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus halobius ruber klebahn 1919]]		[[Category: Bacillus halobius ruber klebahn 1919]]
		+	[[Category: Large Structures]]
	[[Category: Essen, L O]]		[[Category: Essen, L O]]
	[[Category: Oesterhelt, D]]		[[Category: Oesterhelt, D]]

OCA at 09:49, 12 October 2017

OCA — Thu, 12 Oct 2017 09:49:12 GMT

←Older revision		Revision as of 09:49, 12 October 2017
Line 1:		Line 1:
		+
	==Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states==		==Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states==
	<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Halobacterium_salinarum Halobacterium salinarum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://pdbe.org/1tkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp 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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://pdbe.org/1tkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=1tkp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1tkp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1tkp" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ferritin\|Ferritin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halobacterium salinarum~~]]	+	[[Category: Bacillus halobius ruber klebahn 1919]]
	[[Category: Essen, L O]]		[[Category: Essen, L O]]
	[[Category: Oesterhelt, D]]		[[Category: Oesterhelt, D]]

OCA at 11:01, 11 September 2015

OCA — Fri, 11 Sep 2015 11:01:13 GMT

←Older revision		Revision as of 11:01, 11 September 2015
Line 5:		Line 5:
	</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp 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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://pdbe.org/1tkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1tkp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 15:33, 25 December 2014

OCA — Thu, 25 Dec 2014 15:33:40 GMT

←Older revision		Revision as of 15:33, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp 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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPS_HALSA DPS_HALSA]] 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).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
-	[[Category: Essen, L O.]]	+	[[Category: Essen, L O]]
-	[[Category: Oesterhelt, D.]]	+	[[Category: Oesterhelt, D]]
-	[[Category: Offermann, S.]]	+	[[Category: Offermann, S]]
-	[[Category: Zeth, K.]]	+	[[Category: Zeth, K]]
	[[Category: Dpsa]]		[[Category: Dpsa]]
	[[Category: Ferritin]]		[[Category: Ferritin]]

OCA at 08:41, 3 October 2014

OCA — Fri, 03 Oct 2014 08:41:12 GMT

←Older revision		Revision as of 08:41, 3 October 2014
Line 2:		Line 2:
	<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. <br>	+	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKP 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span></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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span></td></tr>
	<table>		<table>
Line 24:		Line 23:
	Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.,Zeth K, Offermann S, Essen LO, Oesterhelt D Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13780-5. Epub 2004 Sep 13. PMID:15365182<ref>PMID:15365182</ref>		Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.,Zeth K, Offermann S, Essen LO, Oesterhelt D Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13780-5. Epub 2004 Sep 13. PMID:15365182<ref>PMID:15365182</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
		+
		+	==See Also==
		+	*[[Ferritin\|Ferritin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:32, 1 May 2014

OCA — Thu, 01 May 2014 09:32:59 GMT

←Older revision		Revision as of 09:32, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. <br>	+	<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. <br>
-	<b>[[Ligand\|Ligands:]]</b> <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
-	<b>[[Related_structure\|Related:]]</b> [[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]<br>	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]</td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span><br>	+	<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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span></td></tr>
		+	<table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
-	[[Image:Consurf_key_small.gif\|right]]	+	[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
Line 17:		Line 18:
	</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/chain_selection.php?pdb_ID=2ata ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.		The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.
Line 23:		Line 25:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:08, 30 April 2014

OCA — Wed, 30 Apr 2014 10:08:29 GMT

←Older revision		Revision as of 10:08, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. <br>		[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. <br>
-	<b>Related:</b> [[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]<br>	+	<b>[[Ligand\|Ligands:]]</b> <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<b>[[Related_structure\|Related:]]</b> [[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]<br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [http://www.ebi.ac.uk/pdbsum/1tkp PDBsum]</span><br>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|right]]		[[Image:Consurf_key_small.gif\|right]]

OCA at 05:31, 30 April 2014

OCA — Wed, 30 Apr 2014 05:31:41 GMT

←Older revision		Revision as of 05:31, 30 April 2014
Line 1:		Line 1:
-	[[Image:~~1tkp~~.~~png~~\|~~left~~\|~~200px~~]]	+	==Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states==
		+	<StructureSection load='1tkp' size='340' side='right' caption='[[1tkp]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	[[1tkp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. <br>
		+	<b>Related:</b> [[1moj\|1moj]], [[1tjo\|1tjo]], [[1tk6\|1tk6]], [[1tko\|1tko]]<br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tk/1tkp_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>
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.

-	~~{{STRUCTURE_1tkp\| PDB=1tkp \| SCENE= }}~~	+	Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.,Zeth K, Offermann S, Essen LO, Oesterhelt D Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13780-5. Epub 2004 Sep 13. PMID:15365182<ref>PMID:15365182</ref>

-	~~===Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis~~ of H.~~salinarum DpsA in its low and high iron states===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-	~~{{ABSTRACT_PUBMED_15365182}}~~	+	<references/>
-		+	__TOC__
-	~~==About this Structure==~~	+	</StructureSection>
-	~~[[1tkp]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA].~~	+
-		+
-	==~~See Also==~~	+
-	*[[Ferritin\|Ferritin]]	+
-		+
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:015365182<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Essen, L O.]]		[[Category: Essen, L O.]]