6amf - Revision history

OCA at 14:20, 4 October 2023

OCA — Wed, 04 Oct 2023 14:20:33 GMT

←Older revision		Revision as of 14:20, 4 October 2023
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	<StructureSection load='6amf' size='340' side='right'caption='[[6amf]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6amf' size='340' side='right'caption='[[6amf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6amf]] 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~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qon 3qon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AMF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6amf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qon 3qon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AMF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</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]] 1.85Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bdc\|3bdc]]~~, [[~~3qoj~~\|~~3qoj]], [[3tp8\|3tp8]], [[3nhh\|3nhh~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6amf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6amf OCA], [https://pdbe.org/6amf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6amf RCSB], [https://www.ebi.ac.uk/pdbsum/6amf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6amf ProSAT]</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=6amf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6amf OCA], [~~http~~://pdbe.org/6amf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6amf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6amf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6amf 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]	+	*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Micrococcal nuclease~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~E., B~~ Garcia-Moreno]]	+	[[Category: Garcia-Moreno E B]]
-	[[Category: Robinson~~, A C~~]]	+	[[Category: Robinson AC]]
-	[[Category: Schlessman~~, J L]]~~	+	[[Category: Schlessman JL]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hyperstable]]~~	+
-	~~[[Category: Ionizable group]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Pdtp~~]]	+

OCA at 08:19, 20 March 2019

OCA — Wed, 20 Mar 2019 08:19:34 GMT

←Older revision		Revision as of 08:19, 20 March 2019
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	==Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/L36E at cryogenic temperature==		==Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/L36E at cryogenic temperature==
-	<StructureSection load='6amf' size='340' side='right' caption='[[6amf]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='6amf' size='340' side='right'caption='[[6amf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6amf]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qon 3qon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6amf]] 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]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qon 3qon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AMF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bdc\|3bdc]], [[3qoj\|3qoj]], [[3tp8\|3tp8]], [[3nhh\|3nhh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bdc\|3bdc]], [[3qoj\|3qoj]], [[3tp8\|3tp8]], [[3nhh\|3nhh]]</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=6amf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6amf OCA], [http://pdbe.org/6amf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6amf RCSB], [http://www.ebi.ac.uk/pdbsum/6amf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6amf ProSAT]</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=6amf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6amf OCA], [http://pdbe.org/6amf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6amf RCSB], [http://www.ebi.ac.uk/pdbsum/6amf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6amf ProSAT]</span></td></tr>
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	== 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.		[[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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thirty years ago, Hwang and Warshel suggested that a microenvironment preorganized to stabilize an ion pair would be incapable of reorganizing to stabilize the reverse ion pair. The implications were that (1) proteins have a limited capacity to reorganize, even under the influence of strong interactions, such as those present when ionizable groups are buried in the hydrophobic interior of a protein, and (2) the inability of proteins to tolerate the reversal of buried ion pairs demonstrates the limitations inherent to continuum electrostatic models of proteins. Previously we showed that when buried individually in the interior of staphylococcal nuclease, Glu23 and Lys36 have p Ka values near pH 7, but when buried simultaneously, they establish a strong interaction of approximately 5 kcal/mol and have p Ka values shifted toward more normal values. Here, using equilibrium thermodynamic measurements, crystal structures, and NMR spectroscopy experiments, we show that although the reversed, individual substitutions-Lys23 and Glu36-also have p Ka values near 7, when buried together, they neither establish a strong interaction nor promote reorganization of their microenvironment. These experiments both confirm Warshel's original hypothesis and expand it by showing that it applies to reorganization, as demonstrated by our artificial ion pairs, as well as to preorganization as is commonly argued for motifs that stabilize naturally occurring ion pairs in polar microenvironments. These data constitute a challenging benchmark useful to test the ability of structure-based algorithms to reproduce the compensation between self-energy, Coulomb and polar interactions in hydrophobic environments of proteins.
		+
		+	Dielectric Properties of a Protein Probed by Reversal of a Buried Ion Pair.,Robinson AC, Schlessman JL, Garcia-Moreno E B J Phys Chem B. 2018 Mar 8;122(9):2516-2524. doi: 10.1021/acs.jpcb.7b12121. Epub, 2018 Feb 21. PMID:29466010<ref>PMID:29466010</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6amf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: E., B Garcia-Moreno]]		[[Category: E., B Garcia-Moreno]]

OCA at 14:46, 6 November 2017

OCA — Mon, 06 Nov 2017 14:46:45 GMT

←Older revision		Revision as of 14:46, 6 November 2017
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	== 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.		[[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.
-
-	==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:23, 6 October 2017

OCA — Fri, 06 Oct 2017 05:23:40 GMT

←Older revision		Revision as of 05:23, 6 October 2017
Line 11:		Line 11:
	== 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.		[[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.
		+
		+	==See Also==
		+	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "6amf" [edit=sysop:move=sysop]

OCA — Wed, 13 Sep 2017 09:38:54 GMT

Protected "6amf" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:38, 13 September 2017

OCA: New page: ==Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/L36E at cryogenic temperature== == Structural highlights ==
<table><tr><td colspan='2'>[[6amf]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qon 3qon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AMF OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AMF FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[3bdc|3bdc]], [[3qoj|3qoj]], [[3tp8|3tp8]], [[3nhh|3nhh]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[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] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6amf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6amf OCA], [http://pdbe.org/6amf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6amf RCSB], [http://www.ebi.ac.uk/pdbsum/6amf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6amf ProSAT]</td></tr>
</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.
TOC
</StructureSection>
[[Category: Micrococcal nuclease]]
[[Category: E., B Garcia-Moreno]]
[[Category: Robinson, A C]]
[[Category: Schlessman, J L]]
[[Category: Hydrolase]]
[[Category: Hyperstable]]
[[Category: Ionizable group]]
[[Category: Nuclease]]
[[Category: Pdtp]]