1k0v - Revision history

OCA at 08:39, 22 May 2024

2024-05-22T08:39:47Z

←Older revision		Revision as of 08:39, 22 May 2024
Line 20:		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=1k0v 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=1k0v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A sequence with a high homology (39% residue identity) with that of the copper-transport CopZ protein from Enterococcus hirae and with the same MXCXXC metal-binding motif has been identified in the genome of Bacillus subtilis, and the corresponding protein has been expressed. The protein, constituted by 73 amino acids, does bind copper(I) under reducing conditions and fully folded in both copper-bound and copper-free forms under the present experimental conditions. The solution structure of the copper-bound form was determined through NMR spectroscopy on an 15N-labeled sample. A total of 1508 meaningful nuclear Overhauser effects, 38 dihedral phi angles, and 48 dihedral psi angles were used in the structural calculations, which lead to a family of 30 conformers with an average rmsd to the mean structure of 0.32 +/- 0.06 A for the backbone and of 0.85 +/- 0.07 A for the heavy atoms. NMR data on the apoprotein also show that, also in this form, the protein is in a folded state and essentially maintains the complete secondary structure. Some disorder is observed in the loop devoted to copper binding. These results are compared with those reported for CopZ from E. hirae whose structure is well-defined only in the apo form. The different behaviors of copper-loaded E. hirae and B. subtilis are tentatively accounted for on the basis of the presence of dithiothreitol used in the latter case, which would stabilize the monomeric form. The comparison is extended to other similar proteins, with particular attention to the copper-binding loop. The nature and the location of conserved residues around the metal-binding site are discussed with respect to their relevance for the metal-binding process. Proposals for the role of CopZ are also presented.
		+
		+	Copper trafficking: the solution structure of Bacillus subtilis CopZ.,Banci L, Bertini I, Del Conte R, Markey J, Ruiz-Duenas FJ Biochemistry. 2001 Dec 25;40(51):15660-8. PMID:11747441<ref>PMID:11747441</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1k0v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:56, 3 April 2024

2024-04-03T07:56:28Z

←Older revision		Revision as of 07:56, 3 April 2024
Line 1:		Line 1:

	==Copper trafficking: the solution structure of Bacillus subtilis CopZ==		==Copper trafficking: the solution structure of Bacillus subtilis CopZ==
-	<StructureSection load='1k0v' size='340' side='right'caption='[[1k0v~~]], [[NMR_Ensembles_of_Models \| 30 NMR models~~]]' scene=''>	+	<StructureSection load='1k0v' size='340' side='right'caption='[[1k0v]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0V 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>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1cpz\|1cpz]]~~<~~/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></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">bscopz ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])~~</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [https://pdbe.org/1k0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [https://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v 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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [https://pdbe.org/1k0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [https://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/COPZ_BACSU COPZ_BACSU]] Chaperone that serves for the intracellular sequestration and transport of Cu(+). Delivers Cu(+) to the copper-transporting ATPase CopA.	+	[https://www.uniprot.org/uniprot/COPZ_BACSU COPZ_BACSU] Chaperone that serves for the intracellular sequestration and transport of Cu(+). Delivers Cu(+) to the copper-transporting ATPase CopA.
	== 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=1k0v 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=1k0v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A sequence with a high homology (39% residue identity) with that of the copper-transport CopZ protein from Enterococcus hirae and with the same MXCXXC metal-binding motif has been identified in the genome of Bacillus subtilis, and the corresponding protein has been expressed. The protein, constituted by 73 amino acids, does bind copper(I) under reducing conditions and fully folded in both copper-bound and copper-free forms under the present experimental conditions. The solution structure of the copper-bound form was determined through NMR spectroscopy on an 15N-labeled sample. A total of 1508 meaningful nuclear Overhauser effects, 38 dihedral phi angles, and 48 dihedral psi angles were used in the structural calculations, which lead to a family of 30 conformers with an average rmsd to the mean structure of 0.32 +/- 0.06 A for the backbone and of 0.85 +/- 0.07 A for the heavy atoms. NMR data on the apoprotein also show that, also in this form, the protein is in a folded state and essentially maintains the complete secondary structure. Some disorder is observed in the loop devoted to copper binding. These results are compared with those reported for CopZ from E. hirae whose structure is well-defined only in the apo form. The different behaviors of copper-loaded E. hirae and B. subtilis are tentatively accounted for on the basis of the presence of dithiothreitol used in the latter case, which would stabilize the monomeric form. The comparison is extended to other similar proteins, with particular attention to the copper-binding loop. The nature and the location of conserved residues around the metal-binding site are discussed with respect to their relevance for the metal-binding process. Proposals for the role of CopZ are also presented.
-
-	Copper trafficking: the solution structure of Bacillus subtilis CopZ.,Banci L, Bertini I, Del Conte R, Markey J, Ruiz-Duenas FJ Biochemistry. 2001 Dec 25;40(51):15660-8. PMID:11747441<ref>PMID:11747441</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1k0v" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banci, L]]	+	[[Category: Banci L]]
-	[[Category: Bertini, I]]	+	[[Category: Bertini I]]
-	[[Category: Conte, R ~~Del~~]]	+	[[Category: Del Conte R]]
-	[[Category: Markey, J]]	+	[[Category: Markey J]]
-	[[Category: Ruiz-Duenas~~, F J]]~~	+	[[Category: Ruiz-Duenas FJ]]
-	~~[[Category: Beta-alpha-beta-beta-alpha-beta]]~~	+
-	~~[[Category: Metal transport~~]]	+

OCA at 08:06, 23 February 2022

2022-02-23T08:06:26Z

←Older revision		Revision as of 08:06, 23 February 2022
Line 3:		Line 3:
	<StructureSection load='1k0v' size='340' side='right'caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>		<StructureSection load='1k0v' size='340' side='right'caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1K0V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0V 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cpz\|1cpz]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cpz\|1cpz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [~~http~~://pdbe.org/1k0v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v 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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [https://pdbe.org/1k0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [https://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/COPZ_BACSU COPZ_BACSU]] Chaperone that serves for the intracellular sequestration and transport of Cu(+). Delivers Cu(+) to the copper-transporting ATPase CopA.	+	[[https://www.uniprot.org/uniprot/COPZ_BACSU COPZ_BACSU]] Chaperone that serves for the intracellular sequestration and transport of Cu(+). Delivers Cu(+) to the copper-transporting ATPase CopA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Banci, L]]		[[Category: Banci, L]]

OCA at 07:38, 25 November 2020

2020-11-25T07:38:49Z

←Older revision		Revision as of 07:38, 25 November 2020
Line 1:		Line 1:

	==Copper trafficking: the solution structure of Bacillus subtilis CopZ==		==Copper trafficking: the solution structure of Bacillus subtilis CopZ==
-	<StructureSection load='1k0v' size='340' side='right' caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>	+	<StructureSection load='1k0v' size='340' side='right'caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1K0V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1K0V 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></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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cpz\|1cpz]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://pdbe.org/1k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v 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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://pdbe.org/1k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/1k0v_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/1k0v_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: Bacillus globigii migula 1900]]		[[Category: Bacillus globigii migula 1900]]
		+	[[Category: Large Structures]]
	[[Category: Banci, L]]		[[Category: Banci, L]]
	[[Category: Bertini, I]]		[[Category: Bertini, I]]

OCA at 07:13, 11 October 2017

2017-10-11T07:13:59Z

←Older revision		Revision as of 07:13, 11 October 2017
Line 1:		Line 1:
		+
	==Copper trafficking: the solution structure of Bacillus subtilis CopZ==		==Copper trafficking: the solution structure of Bacillus subtilis CopZ==
	<StructureSection load='1k0v' size='340' side='right' caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>		<StructureSection load='1k0v' size='340' side='right' caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://pdbe.org/1k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v 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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://pdbe.org/1k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=1k0v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:51, 11 September 2015

2015-09-11T13:51:42Z

←Older revision		Revision as of 13:51, 11 September 2015
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	<StructureSection load='1k0v' size='340' side='right' caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>		<StructureSection load='1k0v' size='340' side='right' caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0V 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v 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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://pdbe.org/1k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		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 1k0v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Banci, L]]		[[Category: Banci, L]]
	[[Category: Bertini, I]]		[[Category: Bertini, I]]

OCA at 17:19, 25 December 2014

2014-12-25T17:19:50Z

←Older revision		Revision as of 17:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0V FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v 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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COPZ_BACSU COPZ_BACSU]] Chaperone that serves for the intracellular sequestration and transport of Cu(+). Delivers Cu(+) to the copper-transporting ATPase CopA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Banci, L.]]	+	[[Category: Banci, L]]
-	[[Category: Bertini, I.]]	+	[[Category: Bertini, I]]
-	[[Category: Conte, R Del.]]	+	[[Category: Conte, R Del]]
-	[[Category: Markey, J.]]	+	[[Category: Markey, J]]
-	[[Category: Ruiz-Duenas, F J.]]	+	[[Category: Ruiz-Duenas, F J]]
	[[Category: Beta-alpha-beta-beta-alpha-beta]]		[[Category: Beta-alpha-beta-beta-alpha-beta]]
	[[Category: Metal transport]]		[[Category: Metal transport]]

OCA at 12:01, 28 September 2014

2014-09-28T12:01:18Z

←Older revision		Revision as of 12:01, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1k0v.~~png~~\|~~left~~\|200px]]	+	==Copper trafficking: the solution structure of Bacillus subtilis CopZ==
		+	<StructureSection load='1k0v' size='340' side='right' caption='[[1k0v]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cpz\|1cpz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bscopz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=1k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0v RCSB], [http://www.ebi.ac.uk/pdbsum/1k0v 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/k0/1k0v_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 ==
		+	A sequence with a high homology (39% residue identity) with that of the copper-transport CopZ protein from Enterococcus hirae and with the same MXCXXC metal-binding motif has been identified in the genome of Bacillus subtilis, and the corresponding protein has been expressed. The protein, constituted by 73 amino acids, does bind copper(I) under reducing conditions and fully folded in both copper-bound and copper-free forms under the present experimental conditions. The solution structure of the copper-bound form was determined through NMR spectroscopy on an 15N-labeled sample. A total of 1508 meaningful nuclear Overhauser effects, 38 dihedral phi angles, and 48 dihedral psi angles were used in the structural calculations, which lead to a family of 30 conformers with an average rmsd to the mean structure of 0.32 +/- 0.06 A for the backbone and of 0.85 +/- 0.07 A for the heavy atoms. NMR data on the apoprotein also show that, also in this form, the protein is in a folded state and essentially maintains the complete secondary structure. Some disorder is observed in the loop devoted to copper binding. These results are compared with those reported for CopZ from E. hirae whose structure is well-defined only in the apo form. The different behaviors of copper-loaded E. hirae and B. subtilis are tentatively accounted for on the basis of the presence of dithiothreitol used in the latter case, which would stabilize the monomeric form. The comparison is extended to other similar proteins, with particular attention to the copper-binding loop. The nature and the location of conserved residues around the metal-binding site are discussed with respect to their relevance for the metal-binding process. Proposals for the role of CopZ are also presented.

-	~~{{STRUCTURE_1k0v\| PDB=1k0v \| SCENE= }}~~	+	Copper trafficking: the solution structure of Bacillus subtilis CopZ.,Banci L, Bertini I, Del Conte R, Markey J, Ruiz-Duenas FJ Biochemistry. 2001 Dec 25;40(51):15660-8. PMID:11747441<ref>PMID:11747441</ref>

-	~~===Copper trafficking:~~ the ~~solution structure of Bacillus subtilis CopZ===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11747441}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1k0v]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011747441<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Banci, L.]]		[[Category: Banci, L.]]

OCA: Protected "1k0v" [edit=sysop:move=sysop]

2012-12-05T11:10:55Z

Protected "1k0v" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:10, 5 December 2012

OCA at 11:10, 5 December 2012

2012-12-05T11:10:52Z

←Older revision		Revision as of 11:10, 5 December 2012
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-	{{Seed}}
	[[Image:1k0v.png\|left\|200px]]		[[Image:1k0v.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1k0v", 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_1k0v\| PDB=1k0v \| SCENE= }}		{{STRUCTURE_1k0v\| PDB=1k0v \| SCENE= }}

	===Copper trafficking: the solution structure of Bacillus subtilis CopZ===		===Copper trafficking: the solution structure of Bacillus subtilis CopZ===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11747441}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11747441 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11747441}}		{{ABSTRACT_PUBMED_11747441}}

	==About this Structure==		==About this Structure==
-	~~1K0V~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA].	+	[[1k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0V OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11747441~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011747441</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Banci, L.]]		[[Category: Banci, L.]]
Line 32:		Line 20:
	[[Category: Beta-alpha-beta-beta-alpha-beta]]		[[Category: Beta-alpha-beta-beta-alpha-beta]]
	[[Category: Metal transport]]		[[Category: Metal transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:01:11 2009''