4zz4 - Revision history

OCA at 15:47, 8 November 2023

OCA — Wed, 08 Nov 2023 15:47:52 GMT

←Older revision		Revision as of 15:47, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution\|Resolution]] 1.798Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [https://pdbe.org/4zz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [https://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [https://pdbe.org/4zz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [https://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:47, 18 May 2023

OCA — Thu, 18 May 2023 07:47:22 GMT

←Older revision		Revision as of 07:47, 18 May 2023
Line 3:		Line 3:
	<StructureSection load='4zz4' size='340' side='right'caption='[[4zz4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4zz4' size='340' side='right'caption='[[4zz4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kf5\|1kf5]]</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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [https://pdbe.org/4zz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [https://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 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/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [~~http~~://pdbe.org/4zz4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>	+	[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 27:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pancreatic ribonuclease]]~~	+	[[Category: Chatake T]]
-	[[Category: Chatake, T]]	+	[[Category: Fujiwara S]]
-	[[Category: Fujiwara, S]]	+
-	~~[[Category: D/h contrast]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ribonuclease some~~]]	+

OCA at 10:49, 9 September 2020

OCA — Wed, 09 Sep 2020 10:49:31 GMT

←Older revision		Revision as of 10:49, 9 September 2020
Line 1:		Line 1:

	==Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method==		==Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method==
-	<StructureSection load='4zz4' size='340' side='right' caption='[[4zz4]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4zz4' size='340' side='right'caption='[[4zz4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kf5\|1kf5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kf5\|1kf5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [http://pdbe.org/4zz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [http://pdbe.org/4zz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
		+	[[Category: Large Structures]]
	[[Category: Pancreatic ribonuclease]]		[[Category: Pancreatic ribonuclease]]
	[[Category: Chatake, T]]		[[Category: Chatake, T]]

OCA at 20:40, 2 December 2018

OCA — Sun, 02 Dec 2018 20:40:56 GMT

←Older revision		Revision as of 20:40, 2 December 2018
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kf5\|1kf5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kf5\|1kf5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [http://pdbe.org/4zz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz4 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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [http://pdbe.org/4zz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4zz4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4zz4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:04, 12 May 2016

OCA — Thu, 12 May 2016 04:04:08 GMT

←Older revision		Revision as of 04:04, 12 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4zz4 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method==
		+	<StructureSection load='4zz4' size='340' side='right' caption='[[4zz4]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4zz4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZZ4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kf5\|1kf5]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=4zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz4 OCA], [http://pdbe.org/4zz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz4 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 A). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

-	~~Authors: Chatake~~, T., Fujiwara, S.	+	A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.,Chatake T, Fujiwara S Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):71-82. doi:, 10.1107/S2059798315021269. Epub 2016 Jan 1. PMID:26894536<ref>PMID:26894536</ref>

-	~~Description: Neutron crystal structure~~ of ~~ribonuclease A determined by~~ the ~~real space D~~/~~H contrast method~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 4zz4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Pancreatic ribonuclease]]
	[[Category: Chatake, T]]		[[Category: Chatake, T]]
	[[Category: Fujiwara, S]]		[[Category: Fujiwara, S]]
		+	[[Category: D/h contrast]]
		+	[[Category: Hydrolase]]
		+	[[Category: Ribonuclease some]]

OCA at 10:49, 30 September 2015

OCA — Wed, 30 Sep 2015 10:49:29 GMT

←Older revision		Revision as of 10:49, 30 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4zz4 is ON HOLD	+	The entry 4zz4 is ON HOLD until Paper Publication

	Authors: Chatake, T., Fujiwara, S.		Authors: Chatake, T., Fujiwara, S.

OCA: Protected "4zz4" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2015 14:56:06 GMT

Protected "4zz4" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:56, 27 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zz4 is ON HOLD Authors: Chatake, T., Fujiwara, S. Description: Neutron crystal structure of ribonuclease A determined by the real space D/H contra...

OCA — Wed, 27 May 2015 14:56:04 GMT

New page: '''Unreleased structure''' The entry 4zz4 is ON HOLD Authors: Chatake, T., Fujiwara, S. Description: Neutron crystal structure of ribonuclease A determined by the real space D/H contra...

New page

'''Unreleased structure'''

The entry 4zz4 is ON HOLD

Authors: Chatake, T., Fujiwara, S.

Description: Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method
[[Category: Unreleased Structures]]
[[Category: Chatake, T]]
[[Category: Fujiwara, S]]