1u9r - Revision history

OCA at 08:44, 14 February 2024

OCA — Wed, 14 Feb 2024 08:44:45 GMT

←Older revision		Revision as of 08:44, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1u9r' size='340' side='right'caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u9r' size='340' side='right'caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U9R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1ey8\|1ey8]]</div></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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">nuc ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [https://pdbe.org/1u9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [https://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r 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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [https://pdbe.org/1u9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [https://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.	+	[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 19:
	</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=1u9r 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=1u9r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The ionizable amino acid side chains of proteins are usually located at the surface. However, in some proteins an ionizable group is embedded in an apolar internal region. Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. Because of the prohibitive energetic cost of transferring a charged group from water to an apolar medium, other stabilizing factors must be invoked, such as ionization-induced water penetration or structural changes. To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dispersions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. This contrasts with a previous cryogenic crystal structure of the V66E mutant, but is consistent with the room-temperature crystal structure reported here. MRD measurements at different pH values show that ionization of Glu-66 or Lys-66 is not accompanied by penetration of long-lived water molecules. On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues.
-
-	Stabilization of internal charges in a protein: water penetration or conformational change?,Denisov VP, Schlessman JL, Garcia-Moreno E B, Halle B Biophys J. 2004 Dec;87(6):3982-94. Epub 2004 Sep 17. PMID:15377517<ref>PMID:15377517</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1u9r" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]		*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Micrococcal nuclease~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: Denisov~~, V P~~]]	+	[[Category: Denisov VP]]
-	[[Category: Garcia-Moreno~~, B E~~]]	+	[[Category: Garcia-Moreno BE]]
-	[[Category: Halle, B]]	+	[[Category: Halle B]]
-	[[Category: Schlessman~~, J L]]~~	+	[[Category: Schlessman JL]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hyperstable variant]]~~	+
-	~~[[Category: Internal water]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Staphylococcal nuclease~~]]	+

OCA at 16:37, 20 October 2021

OCA — Wed, 20 Oct 2021 16:37:03 GMT

←Older revision		Revision as of 16:37, 20 October 2021
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	<StructureSection load='1u9r' size='340' side='right'caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u9r' size='340' side='right'caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1U9R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ey8\|1ey8]]</div></td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ey8\|1ey8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [~~http~~://pdbe.org/1u9r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r 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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [https://pdbe.org/1u9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [https://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.	+	[[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:25, 30 December 2020

OCA — Wed, 30 Dec 2020 07:25:22 GMT

←Older revision		Revision as of 07:25, 30 December 2020
Line 1:		Line 1:

	==Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature==		==Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature==
-	<StructureSection load='1u9r' size='340' side='right' caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1u9r' size='340' side='right'caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1U9R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ey8\|1ey8]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ey8\|1ey8]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://pdbe.org/1u9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r 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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://pdbe.org/1u9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u9/1u9r_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u9/1u9r_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1u9r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1u9r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Denisov, V P]]		[[Category: Denisov, V P]]

OCA at 13:41, 12 October 2017

OCA — Thu, 12 Oct 2017 13:41:39 GMT

←Older revision		Revision as of 13:41, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature==		==Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature==
	<StructureSection load='1u9r' size='340' side='right' caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u9r' size='340' side='right' caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://pdbe.org/1u9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r 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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://pdbe.org/1u9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1u9r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1u9r" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:03, 9 February 2016

OCA — Tue, 09 Feb 2016 17:03:23 GMT

←Older revision		Revision as of 17:03, 9 February 2016
Line 18:		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=1u9r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:20, 11 September 2015

OCA — Fri, 11 Sep 2015 00:20:27 GMT

←Older revision		Revision as of 00:20, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1u9r' size='340' side='right' caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u9r' size='340' side='right' caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U9R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ey8\|1ey8]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ey8\|1ey8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 ~~Staphylococcus~~ aureus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r 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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://pdbe.org/1u9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r 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 1u9r" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
-	[[Category: Staphylococcus aureus]]
	[[Category: Denisov, V P]]		[[Category: Denisov, V P]]
	[[Category: Garcia-Moreno, B E]]		[[Category: Garcia-Moreno, B E]]

OCA at 08:15, 25 December 2014

OCA — Thu, 25 Dec 2014 08:15:42 GMT

←Older revision		Revision as of 08:15, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U9R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ey8\|1ey8]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ey8\|1ey8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r 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=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Denisov, V P.]]	+	[[Category: Denisov, V P]]
-	[[Category: Garcia-Moreno, B E.]]	+	[[Category: Garcia-Moreno, B E]]
-	[[Category: Halle, B.]]	+	[[Category: Halle, B]]
-	[[Category: Schlessman, J L.]]	+	[[Category: Schlessman, J L]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hyperstable variant]]		[[Category: Hyperstable variant]]

OCA at 21:05, 28 September 2014

OCA — Sun, 28 Sep 2014 21:05:43 GMT

←Older revision		Revision as of 21:05, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1u9r.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature==
		+	<StructureSection load='1u9r' size='340' side='right' caption='[[1u9r]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ey8\|1ey8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [http://www.ebi.ac.uk/pdbsum/1u9r 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/u9/1u9r_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 ionizable amino acid side chains of proteins are usually located at the surface. However, in some proteins an ionizable group is embedded in an apolar internal region. Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. Because of the prohibitive energetic cost of transferring a charged group from water to an apolar medium, other stabilizing factors must be invoked, such as ionization-induced water penetration or structural changes. To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dispersions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. This contrasts with a previous cryogenic crystal structure of the V66E mutant, but is consistent with the room-temperature crystal structure reported here. MRD measurements at different pH values show that ionization of Glu-66 or Lys-66 is not accompanied by penetration of long-lived water molecules. On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues.

-	~~{{STRUCTURE_1u9r\| PDB=1u9r \| SCENE= }}~~	+	Stabilization of internal charges in a protein: water penetration or conformational change?,Denisov VP, Schlessman JL, Garcia-Moreno E B, Halle B Biophys J. 2004 Dec;87(6):3982-94. Epub 2004 Sep 17. PMID:15377517<ref>PMID:15377517</ref>

-	~~===Crystal Structure of Staphylococcal Nuclease mutant V66E~~/~~P117G/H124L/S128A at Room Temperature===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15377517}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1u9r]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_aureus Staphylococcus aureus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA].~~	+

	==See Also==		==See Also==
	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]		*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015377517<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

OCA: Protected "1u9r" [edit=sysop:move=sysop]

OCA — Sat, 20 Oct 2012 14:33:14 GMT

Protected "1u9r" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:33, 20 October 2012

OCA at 14:33, 20 October 2012

OCA — Sat, 20 Oct 2012 14:33:12 GMT

←Older revision		Revision as of 14:33, 20 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1u9r.png\|left\|200px]]		[[Image:1u9r.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1u9r", 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_1u9r\| PDB=1u9r \| SCENE= }}		{{STRUCTURE_1u9r\| PDB=1u9r \| SCENE= }}

	===Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature===		===Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15377517}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15377517 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15377517}}		{{ABSTRACT_PUBMED_15377517}}

	==About this Structure==		==About this Structure==
-	~~1U9R~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA].	+	[[1u9r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA].
		+
		+	==See Also==
		+	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15377517~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015377517</ref><references group="xtra"/>
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
Line 30:		Line 21:
	[[Category: Halle, B.]]		[[Category: Halle, B.]]
	[[Category: Schlessman, J L.]]		[[Category: Schlessman, J L.]]
		+	[[Category: Hydrolase]]
	[[Category: Hyperstable variant]]		[[Category: Hyperstable variant]]
	[[Category: Internal water]]		[[Category: Internal water]]
	[[Category: Nuclease]]		[[Category: Nuclease]]
	[[Category: Staphylococcal nuclease]]		[[Category: Staphylococcal nuclease]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:23:16 2009''