7qta - Revision history

OCA at 13:22, 1 February 2024

OCA — Thu, 01 Feb 2024 13:22:31 GMT

←Older revision		Revision as of 13:22, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QTA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QTA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.06Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7qta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qta OCA], [https://pdbe.org/7qta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qta RCSB], [https://www.ebi.ac.uk/pdbsum/7qta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qta 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=7qta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qta OCA], [https://pdbe.org/7qta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qta RCSB], [https://www.ebi.ac.uk/pdbsum/7qta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qta ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:17, 9 November 2022

OCA — Wed, 09 Nov 2022 07:17:44 GMT

←Older revision		Revision as of 07:17, 9 November 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qta is ~~ON HOLD until Paper~~ Publication	+	==S1 nuclease from Aspergillus oryzae in complex with uridine==
		+	<StructureSection load='7qta' size='340' side='right'caption='[[7qta]], [[Resolution\|resolution]] 1.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7qta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QTA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7qta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qta OCA], [https://pdbe.org/7qta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qta RCSB], [https://www.ebi.ac.uk/pdbsum/7qta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qta ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NUS1_ASPOR NUS1_ASPOR] Hydrolyzes only single-stranded DNA and RNA without apparent specificity for bases.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	S1 nuclease from Aspergillus oryzae is a single-strand-specific nuclease from the S1/P1 family that is utilized in biochemistry and biotechnology. S1 nuclease is active on both RNA and DNA but with differing catalytic efficiencies. This study clarifies its catalytic properties using a thorough comparison of differences in the binding of RNA and DNA in the active site of S1 nuclease based on X-ray structures, including two newly solved complexes of S1 nuclease with the products of RNA cleavage at atomic resolution. Conclusions derived from this comparison are valid for the whole S1/P1 nuclease family. For proper model building and refinement, multiple lattice-translocation defects present in the measured diffraction data needed to be solved. Two different approaches were tested and compared. Correction of the measured intensities proved to be superior to the use of the dislocation model of asymmetric units with partial occupancy of individual chains. As the crystals suffered from multiple lattice translocations, equations for their correction were derived de novo. The presented approach to the correction of multiple lattice-translocation defects may help to solve similar problems in the field of protein X-ray crystallography.

-	~~Authors: Adamkova~~, K., Koval, T., ~~Kolenko~~, P., ~~Oestergaard~~, L~~.H.~~, ~~Dohnalek~~, J.	+	Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.,Adamkova K, Koval' T, Ostergaard LH, Duskova J, Maly M, Svecova L, Skalova T, Kolenko P, Dohnalek J Acta Crystallogr D Struct Biol. 2022 Oct 1;78(Pt 10):1194-1209. doi:, 10.1107/S2059798322008397. Epub 2022 Sep 27. PMID:36189740<ref>PMID:36189740</ref>

-	~~Description~~: ~~S1 nuclease from~~ Aspergillus oryzae ~~in complex with uridine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Adamkova, K]]	+	<div class="pdbe-citations 7qta" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kolenko, P~~]]	+	== References ==
-	[[Category: ~~Dohnalek, J~~]]	+	<references/>
-	[[Category: Koval, T]]	+	__TOC__
-	[[Category: Oestergaard~~, L.H~~]]	+	</StructureSection>
		+	[[Category: Aspergillus oryzae RIB40]]
		+	[[Category: Large Structures]]
		+	[[Category: Adamkova K]]
		+	[[Category: Dohnalek J]]
		+	[[Category: Kolenko P]]
		+	[[Category: Koval T]]
		+	[[Category: Oestergaard LH]]

OCA at 08:59, 6 April 2022

OCA — Wed, 06 Apr 2022 08:59:03 GMT

←Older revision		Revision as of 08:59, 6 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7qta is ON HOLD	+	The entry 7qta is ON HOLD until Paper Publication

	Authors: Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J.		Authors: Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J.

OCA: Protected "7qta" [edit=sysop:move=sysop]

OCA — Thu, 27 Jan 2022 05:20:06 GMT

Protected "7qta" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:20, 27 January 2022

OCA: New page: '''Unreleased structure''' The entry 7qta is ON HOLD Authors: Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J. Description: S1 nuclease from Aspergillus oryzae in ...

OCA — Thu, 27 Jan 2022 05:20:05 GMT

New page: '''Unreleased structure''' The entry 7qta is ON HOLD Authors: Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J. Description: S1 nuclease from Aspergillus oryzae in ...

New page

'''Unreleased structure'''

The entry 7qta is ON HOLD

Authors: Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J.

Description: S1 nuclease from Aspergillus oryzae in complex with uridine
[[Category: Unreleased Structures]]
[[Category: Adamkova, K]]
[[Category: Kolenko, P]]
[[Category: Dohnalek, J]]
[[Category: Koval, T]]
[[Category: Oestergaard, L.H]]