5ww6 - Revision history

OCA at 09:19, 20 March 2024

OCA — Wed, 20 Mar 2024 09:19:10 GMT

←Older revision		Revision as of 09:19, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='5ww6' size='340' side='right'caption='[[5ww6]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='5ww6' size='340' side='right'caption='[[5ww6]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ww6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WW6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5WW6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ww6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WW6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WW6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.04Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ww3\|5ww3]], [[5ww4\|5ww4]], [[5ww5\|5ww5]], [[5ww7\|5ww7]], [[5ww8\|5ww8]], [[5ww9\|5ww9]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5ww6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ww6 OCA], [~~http~~://pdbe.org/5ww6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ww6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ww6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ww6 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=5ww6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ww6 OCA], [https://pdbe.org/5ww6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ww6 RCSB], [https://www.ebi.ac.uk/pdbsum/5ww6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ww6 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0QXB7_MYCS2 A0QXB7_MYCS2]
-	DNA-binding proteins under starvation (Dps) are dodecameric nano-compartments for iron oxidation and storage in bacterial cells. These proteins have roughly spherical structures with a hollow interior where iron is stored. Through mutational analysis of a conserved arginine residue in the second Dps protein from Mycobacterium smegmatis, we have identified residues which stabilize the interfaces between the iron entry and ferroxidation sites. Also, we have used X-ray crystallography to determine the structures of co-crystals of iron and Dps in varying proportions and compare the changes in these ligand-bound forms with respect to the apo-protein. The iron-loaded proteins of low, medium and high iron-bound forms were found to exhibit aspartate residues with alternate conformations, some of which could be directly linked to the sites of ferroxidation and iron entry. We conclude that the increased flexibility of aspartates in the presence of iron facilitates its movement from the entry site to the ferroxidaton site, and the two active sites are stabilized by the interactions of a conserved arginine residue R73.	+
-		+
-	Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis.,Williams SM, Chatterji D Metallomics. 2017 Jun 21;9(6):~~685-698. doi: 10.1039~~/~~c7mt00008a. PMID:28418062<ref>PMID:28418062<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5ww6" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chatterji, D~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: ~~Williams, S M~~]]	+	[[Category: Chatterji D]]
-	[[Category: ~~Dna binding]]~~	+	[[Category: Williams SM]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Ferritin-like fold]]~~	+
-	~~[[Category: Ferroxidation]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:18, 7 October 2020

OCA — Wed, 07 Oct 2020 07:18:40 GMT

←Older revision		Revision as of 07:18, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 240 iron atoms per dodecamer==		==Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 240 iron atoms per dodecamer==
-	<StructureSection load='5ww6' size='340' side='right' caption='[[5ww6]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='5ww6' size='340' side='right'caption='[[5ww6]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ww6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WW6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WW6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ww6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WW6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WW6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ww3\|5ww3]], [[5ww4\|5ww4]], [[5ww5\|5ww5]], [[5ww7\|5ww7]], [[5ww8\|5ww8]], [[5ww9\|5ww9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ww3\|5ww3]], [[5ww4\|5ww4]], [[5ww5\|5ww5]], [[5ww7\|5ww7]], [[5ww8\|5ww8]], [[5ww9\|5ww9]]</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=5ww6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ww6 OCA], [http://pdbe.org/5ww6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ww6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ww6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ww6 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=5ww6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ww6 OCA], [http://pdbe.org/5ww6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ww6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ww6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ww6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chatterji, D]]		[[Category: Chatterji, D]]
	[[Category: Williams, S M]]		[[Category: Williams, S M]]

OCA at 09:13, 9 August 2017

OCA — Wed, 09 Aug 2017 09:13:34 GMT

←Older revision		Revision as of 09:13, 9 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ww6 is ~~ON HOLD~~	+	==Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 240 iron atoms per dodecamer==
		+	<StructureSection load='5ww6' size='340' side='right' caption='[[5ww6]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ww6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WW6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ww3\|5ww3]], [[5ww4\|5ww4]], [[5ww5\|5ww5]], [[5ww7\|5ww7]], [[5ww8\|5ww8]], [[5ww9\|5ww9]]</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=5ww6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ww6 OCA], [http://pdbe.org/5ww6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ww6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ww6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ww6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA-binding proteins under starvation (Dps) are dodecameric nano-compartments for iron oxidation and storage in bacterial cells. These proteins have roughly spherical structures with a hollow interior where iron is stored. Through mutational analysis of a conserved arginine residue in the second Dps protein from Mycobacterium smegmatis, we have identified residues which stabilize the interfaces between the iron entry and ferroxidation sites. Also, we have used X-ray crystallography to determine the structures of co-crystals of iron and Dps in varying proportions and compare the changes in these ligand-bound forms with respect to the apo-protein. The iron-loaded proteins of low, medium and high iron-bound forms were found to exhibit aspartate residues with alternate conformations, some of which could be directly linked to the sites of ferroxidation and iron entry. We conclude that the increased flexibility of aspartates in the presence of iron facilitates its movement from the entry site to the ferroxidaton site, and the two active sites are stabilized by the interactions of a conserved arginine residue R73.

-	~~Authors~~:	+	Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis.,Williams SM, Chatterji D Metallomics. 2017 Jun 21;9(6):685-698. doi: 10.1039/c7mt00008a. PMID:28418062<ref>PMID:28418062</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ww6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chatterji, D]]
		+	[[Category: Williams, S M]]
		+	[[Category: Dna binding]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Ferritin-like fold]]
		+	[[Category: Ferroxidation]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5ww6" [edit=sysop:move=sysop]

OCA — Wed, 18 Jan 2017 15:15:52 GMT

Protected "5ww6" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:15, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ww6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Jan 2017 15:15:51 GMT

New page: '''Unreleased structure''' The entry 5ww6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ww6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]