1jok - Revision history

OCA at 08:38, 22 May 2024

2024-05-22T08:38:00Z

←Older revision		Revision as of 08:38, 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=1jok 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=1jok ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L).pdTp.Ca2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 phi, 20 chi 1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 phi, 20 chi 1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (+/- 0.05) A and 0.41 (+/- 0.05) A for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg81-Gly86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg35, Lys84, Tyr85, Arg87, Tyr113, and Tyr115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr113 to change from an extended to a left-handed alpha-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907-1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183-201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.
		+
		+	Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.,Wang J, Truckses DM, Abildgaard F, Dzakula Z, Zolnai Z, Markley JL J Biomol NMR. 1997 Sep;10(2):143-64. PMID:9369015<ref>PMID:9369015</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1jok" 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>

OCA at 07:53, 3 April 2024

2024-04-03T07:53:35Z

←Older revision		Revision as of 07:53, 3 April 2024
Line 1:		Line 1:

	==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==		==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==
-	<StructureSection load='1jok' size='340' side='right'caption='[[1jok~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1jok' size='340' side='right'caption='[[1jok]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jok]] 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jok]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JOK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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">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;'>[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [https://pdbe.org/1jok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [https://www.ebi.ac.uk/pdbsum/1jok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jok 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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [https://pdbe.org/1jok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [https://www.ebi.ac.uk/pdbsum/1jok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jok 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 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=1jok 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=1jok ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L).pdTp.Ca2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 phi, 20 chi 1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 phi, 20 chi 1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (+/- 0.05) A and 0.41 (+/- 0.05) A for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg81-Gly86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg35, Lys84, Tyr85, Arg87, Tyr113, and Tyr115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr113 to change from an extended to a left-handed alpha-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907-1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183-201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.
-
-	Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.,Wang J, Truckses DM, Abildgaard F, Dzakula Z, Zolnai Z, Markley JL J Biomol NMR. 1997 Sep;10(2):143-64. PMID:9369015<ref>PMID:9369015</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1jok" 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: Abildgaard, F]]	+	[[Category: Abildgaard F]]
-	[[Category: Dzakula, Z]]	+	[[Category: Dzakula Z]]
-	[[Category: Markley~~, J L~~]]	+	[[Category: Markley JL]]
-	[[Category: Truckses~~, D M~~]]	+	[[Category: Truckses DM]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	[[Category: Zolnai, Z]]	+	[[Category: Zolnai Z]]
-	~~[[Category: Alpha helix]]~~	+
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ternary complex~~]]	+

OCA at 06:43, 11 August 2021

2021-08-11T06:43:18Z

←Older revision		Revision as of 06:43, 11 August 2021
Line 3:		Line 3:
	<StructureSection load='1jok' size='340' side='right'caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1jok' size='340' side='right'caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jok]] 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jok]] 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JOK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><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">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</div></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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [~~http~~://pdbe.org/1jok PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jok PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jok 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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [https://pdbe.org/1jok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [https://www.ebi.ac.uk/pdbsum/1jok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jok 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]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]	+	*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:06, 6 November 2019

2019-11-06T09:06:05Z

←Older revision		Revision as of 09:06, 6 November 2019
Line 1:		Line 1:

	==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==		==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==
-	<StructureSection load='1jok' size='340' side='right' caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1jok' size='340' side='right'caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jok]] 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jok]] 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1jok" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jok" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Abildgaard, F]]		[[Category: Abildgaard, F]]

OCA at 08:43, 17 January 2018

2018-01-17T08:43:18Z

←Older revision		Revision as of 08:43, 17 January 2018
Line 1:		Line 1:
		+
	==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==		==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==
	<StructureSection load='1jok' size='340' side='right' caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1jok' size='340' side='right' caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://pdbe.org/1jok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok 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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://pdbe.org/1jok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jok ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jo/1jok_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jo/1jok_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1jok" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jok" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:35, 8 February 2016

2016-02-08T19:35:56Z

←Older revision		Revision as of 19:35, 8 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=1jok ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:44, 10 September 2015

2015-09-10T14:44:37Z

←Older revision		Revision as of 14:44, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1jok' size='340' side='right' caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1jok' size='340' side='right' caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jok]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jok]] 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok 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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://pdbe.org/1jok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok 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 1jok" 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: Abildgaard, F]]		[[Category: Abildgaard, F]]
	[[Category: Dzakula, Z]]		[[Category: Dzakula, Z]]

OCA at 01:41, 25 December 2014

2014-12-25T01:41:16Z

←Older revision		Revision as of 01:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jok]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jok]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok 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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok 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]]
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	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Abildgaard, F.]]	+	[[Category: Abildgaard, F]]
-	[[Category: Dzakula, Z.]]	+	[[Category: Dzakula, Z]]
-	[[Category: Markley, J L.]]	+	[[Category: Markley, J L]]
-	[[Category: Truckses, D M.]]	+	[[Category: Truckses, D M]]
-	[[Category: Wang, J.]]	+	[[Category: Wang, J]]
-	[[Category: Zolnai, Z.]]	+	[[Category: Zolnai, Z]]
	[[Category: Alpha helix]]		[[Category: Alpha helix]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Ternary complex]]		[[Category: Ternary complex]]

OCA at 13:09, 28 September 2014

2014-09-28T13:09:11Z

←Older revision		Revision as of 13:09, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1jok.~~png~~\|~~left~~\|200px]]	+	==Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate==
		+	<StructureSection load='1jok' size='340' side='right' caption='[[1jok]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jok]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1joo\|1joo]], [[1joq\|1joq]], [[1jor\|1jor]]</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=1jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jok OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jok RCSB], [http://www.ebi.ac.uk/pdbsum/1jok 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/jo/1jok_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 solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L).pdTp.Ca2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 phi, 20 chi 1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 phi, 20 chi 1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (+/- 0.05) A and 0.41 (+/- 0.05) A for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg81-Gly86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg35, Lys84, Tyr85, Arg87, Tyr113, and Tyr115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr113 to change from an extended to a left-handed alpha-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907-1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183-201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.

-	~~{{STRUCTURE_1jok\| PDB=1jok \| SCENE= }}~~	+	Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.,Wang J, Truckses DM, Abildgaard F, Dzakula Z, Zolnai Z, Markley JL J Biomol NMR. 1997 Sep;10(2):143-64. PMID:9369015<ref>PMID:9369015</ref>

-	~~===Averaged structure for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3'~~,~~5'-bisphosphate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9369015}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1jok]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_aureus Staphylococcus aureus]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1JOK OCA].~~	+

	==See Also==		==See Also==
	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]		*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009369015<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

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

2012-10-20T11:15:14Z

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

←Older revision

Revision as of 11:15, 20 October 2012