2yw7 - Revision history

OCA at 09:07, 25 October 2023

OCA — Wed, 25 Oct 2023 09:07:14 GMT

←Older revision		Revision as of 09:07, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2yw7' size='340' side='right'caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2yw7' size='340' side='right'caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_smegmatis"_trevisan_1889 "bacillus~~ smegmatis~~" trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yw7]] is a 10 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=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~1vei~~\|~~1vei~~]]</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]] 3.3Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [~~http~~://pdbe.org/2yw7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yw7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yw7 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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [https://pdbe.org/2yw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [https://www.ebi.ac.uk/pdbsum/2yw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yw7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~DPS_MYCS2 DPS_MYCS2]~~] 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 ~~(By similarity)~~.	+	[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 ==		== 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 smegmatis trevisan 1889]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chatterji, D]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: Gupta, S]]	+	[[Category: Chatterji D]]
-	[[Category: Roy, S]]	+	[[Category: Gupta S]]
-	[[Category: Saraswathi, R]]	+	[[Category: Roy S]]
-	[[Category: Sekar, K]]	+	[[Category: Saraswathi R]]
-	[[Category: Vijayan, M]]	+	[[Category: Sekar K]]
-	~~[[Category: Dna binding protein]]~~	+	[[Category: Vijayan M]]
-	~~[[Category: Dna-binding protein]]~~	+
-	~~[[Category: Quarternary assebmly~~]]	+

OCA at 13:06, 22 July 2020

OCA — Wed, 22 Jul 2020 13:06:10 GMT

←Older revision		Revision as of 13:06, 22 July 2020
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	==Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps==		==Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps==
-	<StructureSection load='2yw7' size='340' side='right' caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='2yw7' size='340' side='right'caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://pdbe.org/2yw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yw7 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://pdbe.org/2yw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yw7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Ferritin\|Ferritin]]	+	*[[Ferritin 3D structures\|Ferritin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus smegmatis trevisan 1889]]		[[Category: Bacillus smegmatis trevisan 1889]]
		+	[[Category: Large Structures]]
	[[Category: Chatterji, D]]		[[Category: Chatterji, D]]
	[[Category: Gupta, S]]		[[Category: Gupta, S]]

OCA at 09:10, 17 October 2018

OCA — Wed, 17 Oct 2018 09:10:37 GMT

←Older revision		Revision as of 09:10, 17 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps==		==Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps==
	<StructureSection load='2yw7' size='340' side='right' caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2yw7' size='340' side='right' caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://pdbe.org/2yw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://pdbe.org/2yw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yw7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yw/2yw7_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yw/2yw7_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>

OCA at 20:35, 9 February 2016

OCA — Tue, 09 Feb 2016 20:35:34 GMT

←Older revision		Revision as of 20:35, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2yw7' size='340' side='right' caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2yw7' size='340' side='right' caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_smegmatis Mycobacterium~~ smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://pdbe.org/2yw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPS_MYCS2 DPS_MYCS2]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 14:		Line 16:
	<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=2yw7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 26:
	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 2yw7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 31:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycobacterium~~ smegmatis]]	+	[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: Chatterji, D]]		[[Category: Chatterji, D]]
	[[Category: Gupta, S]]		[[Category: Gupta, S]]

OCA at 08:10, 20 January 2015

OCA — Tue, 20 Jan 2015 08:10:10 GMT

←Older revision		Revision as of 08:10, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Mycobacterium smegmatis]]		[[Category: Mycobacterium smegmatis]]
-	[[Category: Chatterji, D.]]	+	[[Category: Chatterji, D]]
-	[[Category: Gupta, S.]]	+	[[Category: Gupta, S]]
-	[[Category: Roy, S.]]	+	[[Category: Roy, S]]
-	[[Category: Saraswathi, R.]]	+	[[Category: Saraswathi, R]]
-	[[Category: Sekar, K.]]	+	[[Category: Sekar, K]]
-	[[Category: Vijayan, M.]]	+	[[Category: Vijayan, M]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Quarternary assebmly]]		[[Category: Quarternary assebmly]]

OCA at 06:48, 29 September 2014

OCA — Mon, 29 Sep 2014 06:48:20 GMT

←Older revision		Revision as of 06:48, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2yw7.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps==
		+	<StructureSection load='2yw7' size='340' side='right' caption='[[2yw7]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YW7 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vei\|1vei]]</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=2yw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yw7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2yw7 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/yw/2yw7_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 ==
		+	Mycobacterium smegmatis Dps degrades spontaneously into a species in which 16 C-terminal residues are cleaved away. A second species, in which all 26 residues constituting the tail were deleted, was cloned, expressed and purified. The first did not bind DNA but formed dodecamers like the native protein, while the second did not bind to DNA and failed to assemble into dodecamers, indicating a role in assembly also for the tail. In the crystal structure of the species without the entire C-terminal tail the molecule has an unusual open decameric structure resulting from the removal of two adjacent subunits from the original dodecameric structure of the native form. A Dps dodecamer could assemble with a dimer or one of two trimers (trimer-A and trimer-B) as intermediate. Trimer-A is the intermediate species in the M. smegmatis protein. Estimation of the surface area buried on trimerization indicates that association within trimer-B is weak. It weakens further when the C-terminal tail is removed, leading to the disruption of the dodecameric structure. Thus, the C-terminal tail has a dual role, one in DNA binding and the other in the assembly of the dodecamer. M. smegmatis Dps also has a short N-terminal tail. A species with nine N-terminal residues deleted formed trimers but not dodecamers in solution, unlike wild-type M. smegmatis Dps, under the same conditions. Unlike in solution, the N-terminal mutant forms dodecamers in the crystal. In native Dps, the N-terminal stretch of one subunit and the C-terminal stretch of a neighboring subunit lock each other into ordered positions. The deletion of one stretch results in the disorder of the other. This disorder appears to result in the formation of a trimeric species of the N-terminal deletion mutant contrary to the indication provided by the native structure. The ferroxidation site is intact in the mutants.

-	~~{{STRUCTURE_2yw7\| PDB=2yw7 \| SCENE= }}~~	+	Role of N and C-terminal tails in DNA binding and assembly in Dps: structural studies of Mycobacterium smegmatis Dps deletion mutants.,Roy S, Saraswathi R, Gupta S, Sekar K, Chatterji D, Vijayan M J Mol Biol. 2007 Jul 20;370(4):752-67. Epub 2007 May 10. PMID:17543333<ref>PMID:17543333</ref>

-	~~===Crystal structure~~ of ~~C-terminal deletion mutant of Mycobacterium smegmatis Dps===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17543333}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2yw7]] is a 10 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].~~	+

	==See Also==		==See Also==
	*[[Ferritin\|Ferritin]]		*[[Ferritin\|Ferritin]]
-	*[[GMP synthase\|GMP synthase]]	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:017543333<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
	[[Category: Mycobacterium smegmatis]]		[[Category: Mycobacterium smegmatis]]
	[[Category: Chatterji, D.]]		[[Category: Chatterji, D.]]

OCA at 15:03, 20 October 2012

OCA — Sat, 20 Oct 2012 15:03:22 GMT

←Older revision		Revision as of 15:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2yw7]] is a 10 chain structure ~~of [[Ferritin]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].	+	[[2yw7]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].

	==See Also==		==See Also==
	*[[Ferritin\|Ferritin]]		*[[Ferritin\|Ferritin]]
		+	*[[GMP synthase\|GMP synthase]]

	==Reference==		==Reference==

OCA: Protected "2yw7" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 17:08:05 GMT

Protected "2yw7" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:08, 26 July 2012

OCA at 17:08, 26 July 2012

OCA — Thu, 26 Jul 2012 17:08:04 GMT

←Older revision		Revision as of 17:08, 26 July 2012
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-	{{Seed}}
	[[Image:2yw7.png\|left\|200px]]		[[Image:2yw7.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2yw7", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2yw7\| PDB=2yw7 \| SCENE= }}		{{STRUCTURE_2yw7\| PDB=2yw7 \| SCENE= }}

	===Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps===		===Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17543333}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17543333 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_17543333}}		{{ABSTRACT_PUBMED_17543333}}

	==About this Structure==		==About this Structure==
-	~~2YW7~~ is a 10 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].	+	[[2yw7]] is a 10 chain structure of [[Ferritin]] with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].
		+
		+	==See Also==
		+	*[[Ferritin\|Ferritin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17543333~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017543333</ref><references group="xtra"/>
	[[Category: Mycobacterium smegmatis]]		[[Category: Mycobacterium smegmatis]]
	[[Category: Chatterji, D.]]		[[Category: Chatterji, D.]]
Line 31:		Line 22:
	[[Category: Sekar, K.]]		[[Category: Sekar, K.]]
	[[Category: Vijayan, M.]]		[[Category: Vijayan, M.]]
		+	[[Category: Dna binding protein]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Quarternary assebmly]]		[[Category: Quarternary assebmly]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:34:12 2009''

OCA at 10:34, 17 February 2009

OCA — Tue, 17 Feb 2009 10:34:13 GMT

←Older revision		Revision as of 10:34, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2YW7 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].	+	2YW7 is a 10 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YW7 OCA].

	==Reference==		==Reference==
-	Role of N and C-terminal tails in DNA binding and assembly in Dps: structural studies of Mycobacterium smegmatis Dps deletion mutants., Roy S, Saraswathi R, Gupta S, Sekar K, Chatterji D, Vijayan M, J Mol Biol. 2007 Jul 20;370(4):752-67. Epub 2007 May 10. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17543333 17543333]~~	+	<ref group="xtra">PMID:17543333</ref><references group="xtra"/>
	[[Category: Mycobacterium smegmatis]]		[[Category: Mycobacterium smegmatis]]
-	[[Category: Single protein]]
	[[Category: Chatterji, D.]]		[[Category: Chatterji, D.]]
	[[Category: Gupta, S.]]		[[Category: Gupta, S.]]
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	[[Category: Quarternary assebmly]]		[[Category: Quarternary assebmly]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 16~~:55:~~58 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:34:12 2009''