5kss - Revision history

OCA at 10:53, 27 September 2023

2023-09-27T10:53:15Z

←Older revision		Revision as of 10:53, 27 September 2023
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	<StructureSection load='5kss' size='340' side='right'caption='[[5kss]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='5kss' size='340' side='right'caption='[[5kss]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kss]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KSS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kss]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xylella_fastidiosa_9a5c Xylella fastidiosa 9a5c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KSS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.82Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5kst\|5kst]], [[5ksq\|5ksq]], [[5ksr\|5ksr]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class="sblockDat"><span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5]~~ </~~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=5kss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kss OCA], [https://pdbe.org/5kss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kss RCSB], [https://www.ebi.ac.uk/pdbsum/5kss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kss 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=5kss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kss OCA], [~~http~~://pdbe.org/5kss PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kss RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kss PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kss ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SURE_XYLFA SURE_XYLFA]] Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates.	+	[https://www.uniprot.org/uniprot/SURE_XYLFA SURE_XYLFA] Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 5'-nucleotidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Aparicio, R~~]]	+	[[Category: Xylella fastidiosa 9a5c]]
-	[[Category: ~~Fonseca, E M.B~~]]	+	[[Category: Aparicio R]]
-	[[Category: ~~Iulek, J~~]]	+	[[Category: De Souza AP]]
-	[[Category: ~~Machado, A T.P~~]]	+	[[Category: De Toledo AMS]]
-	[[Category: ~~Polikarpov, I~~]]	+	[[Category: Dos Reis MA]]
-	[[Category: ~~Reis, M A.~~Dos]]	+	[[Category: Dos Santos CA]]
-	~~[[Category:~~ Santos~~, C A.Dos~~]]	+	[[Category: Fonseca EMB]]
-	[[Category: ~~Saraiva, A M~~]]	+	[[Category: Iulek J]]
-	[[Category: ~~Souza, A P.De~~]]	+	[[Category: Machado ATP]]
-	[[Category: ~~Toledo, A M.S De~~]]	+	[[Category: Polikarpov I]]
-	[[Category: ~~Crystallization~~]]	+	[[Category: Saraiva AM]]
-	[[Category: ~~Hydrolase]]~~	+
-	~~[[Category: Xylella fastidiosa~~]]	+

OCA at 06:33, 5 August 2020

2020-08-05T06:33:36Z

←Older revision		Revision as of 06:33, 5 August 2020
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	==Stationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-Ds (Dimer Smaller)==		==Stationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-Ds (Dimer Smaller)==
-	<StructureSection load='5kss' size='340' side='right' caption='[[5kss]], [[Resolution\|resolution]] 2.82Å' scene=''>	+	<StructureSection load='5kss' size='340' side='right'caption='[[5kss]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kss]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KSS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kss]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KSS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kst\|5kst]], [[5ksq\|5ksq]], [[5ksr\|5ksr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kst\|5kst]], [[5ksq\|5ksq]], [[5ksr\|5ksr]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=5kss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kss OCA], [http://pdbe.org/5kss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kss RCSB], [http://www.ebi.ac.uk/pdbsum/5kss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kss 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=5kss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kss OCA], [http://pdbe.org/5kss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kss RCSB], [http://www.ebi.ac.uk/pdbsum/5kss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kss ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 5'-nucleotidase]]		[[Category: 5'-nucleotidase]]
		+	[[Category: Large Structures]]
	[[Category: Aparicio, R]]		[[Category: Aparicio, R]]
	[[Category: Fonseca, E M.B]]		[[Category: Fonseca, E M.B]]

OCA at 04:03, 4 August 2017

2017-08-04T04:03:00Z

←Older revision		Revision as of 04:03, 4 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kss is ~~ON HOLD until Paper~~ Publication	+	==Stationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-Ds (Dimer Smaller)==
		+	<StructureSection load='5kss' size='340' side='right' caption='[[5kss]], [[Resolution\|resolution]] 2.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kss]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KSS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kst\|5kst]], [[5ksq\|5ksq]], [[5ksr\|5ksr]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </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=5kss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kss OCA], [http://pdbe.org/5kss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kss RCSB], [http://www.ebi.ac.uk/pdbsum/5kss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kss ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SURE_XYLFA SURE_XYLFA]] Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein.

-	~~Authors: Machado~~, ~~A.T.P~~., Fonseca, ~~E.M.B., Dos~~ Reis~~, M.A.~~, Saraiva, ~~A.M., Dos~~ Santos, ~~C.A., De~~ Toledo~~, A.M.S.~~, Polikarpov, I., De Souza~~, A.P.~~, Aparicio, R., Iulek, J.	+	Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.,Machado ATP, Fonseca EMB, Reis MAD, Saraiva AM, Santos CAD, de Toledo MAS, Polikarpov I, de Souza AP, Aparicio R, Iulek J Proteins. 2017 Jul 5. doi: 10.1002/prot.25347. PMID:28677327<ref>PMID:28677327</ref>

-	~~Description: Stationary phase survival protein E (SurE) from Xylella fastidiosa~~ -~~XFSurE~~-~~Ds (Dimer Smaller)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kss" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 5'-nucleotidase]]
	[[Category: Aparicio, R]]		[[Category: Aparicio, R]]
-	[[Category: ~~De Souza, A.P]]~~	+	[[Category: Fonseca, E M.B]]
-	~~[[Category: Machado, A.T.P]]~~	+
-	~~[[Category: Polikarpov, I]]~~	+
-	~~[[Category: Dos Reis~~, M.A]]	+
	[[Category: Iulek, J]]		[[Category: Iulek, J]]
-	[[Category: ~~De Toledo~~, A.~~M.S~~]]	+	[[Category: Machado, A T.P]]
-	[[Category: ~~Saraiva~~, A.M]]	+	[[Category: Polikarpov, I]]
-	[[Category: ~~Dos~~ Santos, C.A]]	+	[[Category: Reis, M A.Dos]]
-	[[Category: ~~Fonseca~~, E.M.B]]	+	[[Category: Santos, C A.Dos]]
		+	[[Category: Saraiva, A M]]
		+	[[Category: Souza, A P.De]]
		+	[[Category: Toledo, A M.S De]]
		+	[[Category: Crystallization]]
		+	[[Category: Hydrolase]]
		+	[[Category: Xylella fastidiosa]]

OCA at 10:24, 9 March 2017

2017-03-09T10:24:31Z

←Older revision		Revision as of 10:24, 9 March 2017
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	Description: Stationary phase survival protein E (SurE) from Xylella fastidiosa -XFSurE-Ds (Dimer Smaller)		Description: Stationary phase survival protein E (SurE) from Xylella fastidiosa -XFSurE-Ds (Dimer Smaller)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Aparicio, R]]
	[[Category: De Souza, A.P]]		[[Category: De Souza, A.P]]
	[[Category: Machado, A.T.P]]		[[Category: Machado, A.T.P]]
	[[Category: Polikarpov, I]]		[[Category: Polikarpov, I]]
-	[[Category: Dos Santos, C.A]]
-	[[Category: Aparicio, R]]
	[[Category: Dos Reis, M.A]]		[[Category: Dos Reis, M.A]]
	[[Category: Iulek, J]]		[[Category: Iulek, J]]
	[[Category: De Toledo, A.M.S]]		[[Category: De Toledo, A.M.S]]
	[[Category: Saraiva, A.M]]		[[Category: Saraiva, A.M]]
		+	[[Category: Dos Santos, C.A]]
	[[Category: Fonseca, E.M.B]]		[[Category: Fonseca, E.M.B]]

OCA at 14:20, 9 September 2016

2016-09-09T14:20:17Z

←Older revision		Revision as of 14:20, 9 September 2016
Line 3:		Line 3:
	The entry 5kss is ON HOLD until Paper Publication		The entry 5kss is ON HOLD until Paper Publication

-	Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, M.A.S., Polikarpov, I., De Souza, A.P., Aparicio, R., ~~Lulek~~, J.	+	Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, A.M.S., Polikarpov, I., De Souza, A.P., Aparicio, R., Iulek, J.

	Description: Stationary phase survival protein E (SurE) from Xylella fastidiosa -XFSurE-Ds (Dimer Smaller)		Description: Stationary phase survival protein E (SurE) from Xylella fastidiosa -XFSurE-Ds (Dimer Smaller)
Line 11:		Line 11:
	[[Category: Polikarpov, I]]		[[Category: Polikarpov, I]]
	[[Category: Dos Santos, C.A]]		[[Category: Dos Santos, C.A]]
-	[[Category: De Toledo, M.A.S]]
-	[[Category: Lulek, J]]
	[[Category: Aparicio, R]]		[[Category: Aparicio, R]]
	[[Category: Dos Reis, M.A]]		[[Category: Dos Reis, M.A]]
		+	[[Category: Iulek, J]]
		+	[[Category: De Toledo, A.M.S]]
	[[Category: Saraiva, A.M]]		[[Category: Saraiva, A.M]]
	[[Category: Fonseca, E.M.B]]		[[Category: Fonseca, E.M.B]]

OCA at 02:01, 4 August 2016

2016-08-04T02:01:08Z

←Older revision		Revision as of 02:01, 4 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kss is ON HOLD	+	The entry 5kss is ON HOLD until Paper Publication

	Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, M.A.S., Polikarpov, I., De Souza, A.P., Aparicio, R., Lulek, J.		Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, M.A.S., Polikarpov, I., De Souza, A.P., Aparicio, R., Lulek, J.

OCA: Protected "5kss" [edit=sysop:move=sysop]

2016-07-26T12:49:50Z

Protected "5kss" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:49, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kss is ON HOLD Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, M.A.S., Polikarpov, I., De So...

2016-07-26T12:49:49Z

New page: '''Unreleased structure''' The entry 5kss is ON HOLD Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, M.A.S., Polikarpov, I., De So...

New page

'''Unreleased structure'''

The entry 5kss is ON HOLD

Authors: Machado, A.T.P., Fonseca, E.M.B., Dos Reis, M.A., Saraiva, A.M., Dos Santos, C.A., De Toledo, M.A.S., Polikarpov, I., De Souza, A.P., Aparicio, R., Lulek, J.

Description: Stationary phase survival protein E (SurE) from Xylella fastidiosa -XFSurE-Ds (Dimer Smaller)
[[Category: Unreleased Structures]]
[[Category: De Souza, A.P]]
[[Category: Machado, A.T.P]]
[[Category: Polikarpov, I]]
[[Category: Dos Santos, C.A]]
[[Category: De Toledo, M.A.S]]
[[Category: Lulek, J]]
[[Category: Aparicio, R]]
[[Category: Dos Reis, M.A]]
[[Category: Saraiva, A.M]]
[[Category: Fonseca, E.M.B]]