3dso - Revision history

OCA at 08:24, 20 March 2024

OCA — Wed, 20 Mar 2024 08:24:22 GMT

←Older revision		Revision as of 08:24, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3dso' size='340' side='right'caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='3dso' size='340' side='right'caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cupriavidus_metallidurans_ch34~~ Cupriavidus metallidurans ~~ch34~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_metallidurans_CH34 Cupriavidus metallidurans CH34]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DSO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>~~, ~~<scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 1.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2k0q\|2k0q]], [[3dsp\|3dsp]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">copK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 Cupriavidus metallidurans CH34])~~</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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [https://pdbe.org/3dso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [https://www.ebi.ac.uk/pdbsum/3dso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dso 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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [https://pdbe.org/3dso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [https://www.ebi.ac.uk/pdbsum/3dso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dso ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~COPK_RALME COPK_RALME]~~] Involved in resistance to copper. Can bind up to 2 copper ions. Has higher affinity for Cu(+) than for Cu(2+).<ref>PMID:18533181</ref>	+	[https://www.uniprot.org/uniprot/COPK_CUPMC COPK_CUPMC] Involved in resistance to copper. Can bind up to 2 copper ions. Has higher affinity for Cu(+) than for Cu(2+).<ref>PMID:18533181</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=3dso 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=3dso ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The bacterium Cupriavidus metallidurans CH34 is resistant to high environmental concentrations of many metal ions, including copper. This ability arises primarily from the presence of a large plasmid pMOL30 which includes a cluster of 19 cop genes that respond to copper. One of the protein products CopK is induced at high levels and is expressed to the periplasm as a small soluble protein (8.3 kDa). Apo-CopK associates in solution to form a dimer (K(D) approximately 10(-5) M) whose structure was defined by NMR and X-ray crystallography. The individual molecules feature two antiparallel beta-sheets arranged in a sandwich-like structure and interact through C-terminal beta-strands. It binds Cu(II) with low affinity (K(D)(Cu(II)) > 10(-6) M) but Cu(I) with high affinity (K(D)(Cu(I)) = 2 x 10(-11) M). Cu(I)-CopK was also a dimer in the solid state and featured a distorted tetrahedral site Cu(I)(S-Met)(3)(NCS). The isothiocyanato ligand originated from the crystallization solution. Binding of Cu(I) or Ag(I), but not of Cu(II), favored the monomeric form in solution. While Ag(I)-CopK was stable as isolated, Cu(I)-CopK was moderately air-sensitive due to a strong binding cooperativity between Cu(I) and Cu(II). This was documented by determination of the Cu(I) and Cu(II) binding affinities in the presence of the other ion: K(D)(Cu(I)) = 2 x 10(-13) M and K(D)(Cu(II)) = 3 x 10(-12) M, that is, binding of Cu(II) increased the affinity for Cu(I) by a factor of approximately 10(2) and binding of Cu(I) increased the affinity for Cu(II) by a factor of at least 10(6). Stable forms of both Cu(I)Cu(II)-CopK and Ag(I)Cu(II)-CopK were isolated readily. Consistent with this unprecedented copper binding chemistry, NMR spectroscopy detected three distinct forms: apo-CopK, Cu(I)-CopK and Cu(I)Cu(II)-CopK that do not exchange on the NMR time scale. This information provides a valuable guide to the role of CopK in copper resistance.
-
-	Unprecedented Binding Cooperativity between Cu(I) and Cu(II) in the Copper Resistance Protein CopK from Cupriavidus metallidurans CH34: Implications from Structural Studies by NMR Spectroscopy and X-Ray Crystallography.,Chong LX, Ash MR, Maher MJ, Hinds MG, Xiao Z, Wedd AG J Am Chem Soc. 2009 Feb 24. PMID:19236095<ref>PMID:19236095</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3dso" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cupriavidus metallidurans ~~ch34~~]]	+	[[Category: Cupriavidus metallidurans CH34]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ash, M R]]	+	[[Category: Ash M-R]]
-	[[Category: Maher~~, M J]]~~	+	[[Category: Maher MJ]]
-	~~[[Category: Copper resistance]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 08:06, 9 February 2022

OCA — Wed, 09 Feb 2022 08:06:49 GMT

←Older revision		Revision as of 08:06, 9 February 2022
Line 1:		Line 1:

	==Crystal structure of Cu(I) bound copper resistance protein CopK==		==Crystal structure of Cu(I) bound copper resistance protein CopK==
-	<StructureSection load='3dso' size='340' side='right' caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='3dso' size='340' side='right'caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cupriavidus_metallidurans_ch34 Cupriavidus metallidurans ch34]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_metallidurans_ch34 Cupriavidus metallidurans ch34]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DSO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2k0q\|2k0q]], [[3dsp\|3dsp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2k0q\|2k0q]], [[3dsp\|3dsp]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 Cupriavidus metallidurans CH34])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 Cupriavidus metallidurans CH34])</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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [~~http~~://pdbe.org/3dso PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dso PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dso 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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [https://pdbe.org/3dso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [https://www.ebi.ac.uk/pdbsum/3dso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dso ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/COPK_RALME COPK_RALME]] Involved in resistance to copper. Can bind up to 2 copper ions. Has higher affinity for Cu(+) than for Cu(2+).<ref>PMID:18533181</ref>	+	[[https://www.uniprot.org/uniprot/COPK_RALME COPK_RALME]] Involved in resistance to copper. Can bind up to 2 copper ions. Has higher affinity for Cu(+) than for Cu(2+).<ref>PMID:18533181</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ds/3dso_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ds/3dso_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Cupriavidus metallidurans ch34]]		[[Category: Cupriavidus metallidurans ch34]]
		+	[[Category: Large Structures]]
	[[Category: Ash, M R]]		[[Category: Ash, M R]]
	[[Category: Maher, M J]]		[[Category: Maher, M J]]
	[[Category: Copper resistance]]		[[Category: Copper resistance]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]

OCA at 08:55, 25 October 2017

OCA — Wed, 25 Oct 2017 08:55:52 GMT

←Older revision		Revision as of 08:55, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of Cu(I) bound copper resistance protein CopK==		==Crystal structure of Cu(I) bound copper resistance protein CopK==
	<StructureSection load='3dso' size='340' side='right' caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='3dso' size='340' side='right' caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2k0q\|2k0q]], [[3dsp\|3dsp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2k0q\|2k0q]], [[3dsp\|3dsp]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 Cupriavidus metallidurans CH34])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 Cupriavidus metallidurans CH34])</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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [http://pdbe.org/3dso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [http://www.ebi.ac.uk/pdbsum/3dso 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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [http://pdbe.org/3dso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [http://www.ebi.ac.uk/pdbsum/3dso PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dso ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 16:49, 7 February 2016

OCA — Sun, 07 Feb 2016 16:49:56 GMT

←Older revision		Revision as of 16:49, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3dso' size='340' side='right' caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='3dso' size='340' side='right' caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cupriavidus_metallidurans~~ Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans_ch34 Cupriavidus metallidurans ch34]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DSO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2k0q\|2k0q]], [[3dsp\|3dsp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2k0q\|2k0q]], [[3dsp\|3dsp]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~119219~~ Cupriavidus metallidurans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266264 Cupriavidus metallidurans CH34])</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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [http://www.ebi.ac.uk/pdbsum/3dso 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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [http://pdbe.org/3dso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [http://www.ebi.ac.uk/pdbsum/3dso PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COPK_RALME COPK_RALME]] Involved in resistance to copper. Can bind up to 2 copper ions. Has higher affinity for Cu(+) than for Cu(2+).<ref>PMID:18533181</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		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=3dso ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 28:
	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 3dso" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cupriavidus metallidurans]]	+	[[Category: Cupriavidus metallidurans ch34]]
	[[Category: Ash, M R]]		[[Category: Ash, M R]]
	[[Category: Maher, M J]]		[[Category: Maher, M J]]
	[[Category: Copper resistance]]		[[Category: Copper resistance]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]

OCA at 08:19, 12 November 2014

OCA — Wed, 12 Nov 2014 08:19:05 GMT

←Older revision		Revision as of 08:19, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3dso.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Cu(I) bound copper resistance protein CopK==
		+	<StructureSection load='3dso' size='340' side='right' caption='[[3dso]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dso]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DSO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2k0q\|2k0q]], [[3dsp\|3dsp]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">copK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=119219 Cupriavidus metallidurans])</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=3dso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dso OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dso RCSB], [http://www.ebi.ac.uk/pdbsum/3dso 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/ds/3dso_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 bacterium Cupriavidus metallidurans CH34 is resistant to high environmental concentrations of many metal ions, including copper. This ability arises primarily from the presence of a large plasmid pMOL30 which includes a cluster of 19 cop genes that respond to copper. One of the protein products CopK is induced at high levels and is expressed to the periplasm as a small soluble protein (8.3 kDa). Apo-CopK associates in solution to form a dimer (K(D) approximately 10(-5) M) whose structure was defined by NMR and X-ray crystallography. The individual molecules feature two antiparallel beta-sheets arranged in a sandwich-like structure and interact through C-terminal beta-strands. It binds Cu(II) with low affinity (K(D)(Cu(II)) > 10(-6) M) but Cu(I) with high affinity (K(D)(Cu(I)) = 2 x 10(-11) M). Cu(I)-CopK was also a dimer in the solid state and featured a distorted tetrahedral site Cu(I)(S-Met)(3)(NCS). The isothiocyanato ligand originated from the crystallization solution. Binding of Cu(I) or Ag(I), but not of Cu(II), favored the monomeric form in solution. While Ag(I)-CopK was stable as isolated, Cu(I)-CopK was moderately air-sensitive due to a strong binding cooperativity between Cu(I) and Cu(II). This was documented by determination of the Cu(I) and Cu(II) binding affinities in the presence of the other ion: K(D)(Cu(I)) = 2 x 10(-13) M and K(D)(Cu(II)) = 3 x 10(-12) M, that is, binding of Cu(II) increased the affinity for Cu(I) by a factor of approximately 10(2) and binding of Cu(I) increased the affinity for Cu(II) by a factor of at least 10(6). Stable forms of both Cu(I)Cu(II)-CopK and Ag(I)Cu(II)-CopK were isolated readily. Consistent with this unprecedented copper binding chemistry, NMR spectroscopy detected three distinct forms: apo-CopK, Cu(I)-CopK and Cu(I)Cu(II)-CopK that do not exchange on the NMR time scale. This information provides a valuable guide to the role of CopK in copper resistance.

-	~~{{STRUCTURE_3dso\| PDB=3dso \| SCENE= }}~~	+	Unprecedented Binding Cooperativity between Cu(I) and Cu(II) in the Copper Resistance Protein CopK from Cupriavidus metallidurans CH34: Implications from Structural Studies by NMR Spectroscopy and X-Ray Crystallography.,Chong LX, Ash MR, Maher MJ, Hinds MG, Xiao Z, Wedd AG J Am Chem Soc. 2009 Feb 24. PMID:19236095<ref>PMID:19236095</ref>

-	~~===Crystal structure~~ of ~~Cu(I) bound copper resistance protein CopK===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19236095}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3dso]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019236095<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Cupriavidus metallidurans]]		[[Category: Cupriavidus metallidurans]]
-	[[Category: Ash, M R.]]	+	[[Category: Ash, M R]]
-	[[Category: Maher, M J.]]	+	[[Category: Maher, M J]]
	[[Category: Copper resistance]]		[[Category: Copper resistance]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]

OCA: Protected "3dso" [edit=sysop:move=sysop]

OCA — Wed, 09 Jan 2013 09:04:41 GMT

Protected "3dso" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:04, 9 January 2013

OCA at 09:04, 9 January 2013

OCA — Wed, 09 Jan 2013 09:04:37 GMT

←Older revision		Revision as of 09:04, 9 January 2013
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-	{{Seed}}
	[[Image:3dso.png\|left\|200px]]		[[Image:3dso.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dso", 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),
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	{{STRUCTURE_3dso\| PDB=3dso \| SCENE= }}		{{STRUCTURE_3dso\| PDB=3dso \| SCENE= }}

	===Crystal structure of Cu(I) bound copper resistance protein CopK===		===Crystal structure of Cu(I) bound copper resistance protein CopK===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19236095}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19236095 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19236095}}		{{ABSTRACT_PUBMED_19236095}}

	==About this Structure==		==About this Structure==
-	~~3DSO~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].	+	[[3dso]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19236095~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019236095</ref><references group="xtra"/>
	[[Category: Cupriavidus metallidurans]]		[[Category: Cupriavidus metallidurans]]
	[[Category: Ash, M R.]]		[[Category: Ash, M R.]]
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	[[Category: Copper resistance]]		[[Category: Copper resistance]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
-	[[Category: Periplasm]]
-	[[Category: Plasmid]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:40:26 2010''

OCA at 08:31, 22 September 2010

OCA — Wed, 22 Sep 2010 08:31:28 GMT

←Older revision		Revision as of 08:31, 22 September 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3DSO is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].	+	3DSO is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].

	==Reference==		==Reference==
-	Unprecedented Binding Cooperativity between Cu(I) and Cu(II) in the Copper Resistance Protein CopK from Cupriavidus metallidurans CH34: Implications from Structural Studies by NMR Spectroscopy and X-Ray Crystallography., Chong LX, Ash MR, Maher MJ, Hinds MG, Xiao Z, Wedd AG, J Am Chem Soc. 2009 Feb 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19236095 19236095]~~	+	<ref group="xtra">PMID:19236095</ref><references group="xtra"/>
	[[Category: Cupriavidus metallidurans]]		[[Category: Cupriavidus metallidurans]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Ash, M R.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx:audit_author~~.]]	+	[[Category: Maher, M J.]]
	[[Category: Copper resistance]]		[[Category: Copper resistance]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
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	[[Category: Plasmid]]		[[Category: Plasmid]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 25 21~~:05:~~23 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:40:26 2010''

OCA at 19:05, 25 March 2009

OCA — Wed, 25 Mar 2009 19:05:24 GMT

←Older revision		Revision as of 19:05, 25 March 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3DSO is a ~~1 chain~~ structure of sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].	+	3DSO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cupriavidus_metallidurans Cupriavidus metallidurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DSO OCA].

	==Reference==		==Reference==
-	~~<ref group="xtra">~~PMID:~~19236095<~~/~~ref><references group="xtra"~~/>	+	Unprecedented Binding Cooperativity between Cu(I) and Cu(II) in the Copper Resistance Protein CopK from Cupriavidus metallidurans CH34: Implications from Structural Studies by NMR Spectroscopy and X-Ray Crystallography., Chong LX, Ash MR, Maher MJ, Hinds MG, Xiao Z, Wedd AG, J Am Chem Soc. 2009 Feb 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19236095 19236095]
	[[Category: Cupriavidus metallidurans]]		[[Category: Cupriavidus metallidurans]]
-	[[Category: ~~Ash, M R.~~]]	+	[[Category: Single protein]]
-	[[Category: ~~Maher~~, ~~M J~~.]]	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
	[[Category: Copper resistance]]		[[Category: Copper resistance]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
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	[[Category: Plasmid]]		[[Category: Plasmid]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 11:28:56 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 21:05:23 2009''

OCA at 09:28, 25 March 2009

OCA — Wed, 25 Mar 2009 09:28:57 GMT

←Older revision		Revision as of 09:28, 25 March 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3dso.~~jpg~~\|left\|200px]]	+	[[Image:3dso.png\|left\|200px]]

	<!--		<!--
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	[[Category: Plasmid]]		[[Category: Plasmid]]

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