6zhn - Revision history

OCA at 16:03, 14 March 2024

OCA — Thu, 14 Mar 2024 16:03:59 GMT

←Older revision		Revision as of 16:03, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/THM1_THADA THM1_THADA] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.		[https://www.uniprot.org/uniprot/THM1_THADA THM1_THADA] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, a low-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.
-
-	Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals.,Blum TB, Housset D, Clabbers MTB, van Genderen E, Bacia-Verloop M, Zander U, McCarthy AA, Schoehn G, Ling WL, Abrahams JP Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):75-85. doi:, 10.1107/S2059798320014540. Epub 2021 Jan 1. PMID:33404527<ref>PMID:33404527</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6zhn" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:49, 24 January 2024

OCA — Wed, 24 Jan 2024 13:49:53 GMT

←Older revision		Revision as of 13:49, 24 January 2024
Line 1:		Line 1:

	==3D electron diffraction structure of thaumatin from Thaumatococcus daniellii==		==3D electron diffraction structure of thaumatin from Thaumatococcus daniellii==
-	<StructureSection load='6zhn' size='340' side='right'caption='[[6zhn]]' scene=''>	+	<StructureSection load='6zhn' size='340' side='right'caption='[[6zhn]], [[Resolution\|resolution]] 2.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zhn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHN FirstGlance]. <br>
-	</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=6zhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhn OCA], [https://pdbe.org/6zhn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhn RCSB], [https://www.ebi.ac.uk/pdbsum/6zhn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhn ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron crystallography, [[Resolution\|Resolution]] 2.76Å</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></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=6zhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhn OCA], [https://pdbe.org/6zhn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhn RCSB], [https://www.ebi.ac.uk/pdbsum/6zhn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/THM1_THADA THM1_THADA] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, a low-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.
		+
		+	Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals.,Blum TB, Housset D, Clabbers MTB, van Genderen E, Bacia-Verloop M, Zander U, McCarthy AA, Schoehn G, Ling WL, Abrahams JP Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):75-85. doi:, 10.1107/S2059798320014540. Epub 2021 Jan 1. PMID:33404527<ref>PMID:33404527</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zhn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Thaumatococcus daniellii]]
	[[Category: Abrahams JP]]		[[Category: Abrahams JP]]
	[[Category: Blum T]]		[[Category: Blum T]]

OCA at 07:55, 27 January 2021

OCA — Wed, 27 Jan 2021 07:55:56 GMT

←Older revision		Revision as of 07:55, 27 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zhn ~~is ON HOLD until Paper Publication~~	+	==3D electron diffraction structure of thaumatin from Thaumatococcus daniellii==
-		+	<StructureSection load='6zhn' size='340' side='right'caption='[[6zhn]]' scene=''>
-	~~Authors~~: ~~Blum, T~~.~~, Housset, D~~., ~~Clabbers, M~~.T.B., ~~van Genderen, E~~., ~~Schoehn, G~~., ~~Ling, W~~.L., ~~Abrahams, J~~.P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHN FirstGlance]. <br>
-	~~Description: 3D electron diffraction structure of thaumatin from Thaumatococcus daniellii~~	+	</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=6zhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhn OCA], [https://pdbe.org/6zhn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhn RCSB], [https://www.ebi.ac.uk/pdbsum/6zhn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Abrahams~~, J.P~~]]	+	__TOC__
-	[[Category: ~~Housset, D~~]]	+	</StructureSection>
-	[[Category: ~~Schoehn, G~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Van Genderen, E~~]]	+	[[Category: Abrahams JP]]
-	[[Category: Ling~~, W.L~~]]	+	[[Category: Blum T]]
-	[[Category: ~~Clabbers, M.T.B~~]]	+	[[Category: Clabbers MTB]]
-	[[Category: ~~Blum, T~~]]	+	[[Category: Housset D]]
		+	[[Category: Ling WL]]
		+	[[Category: Schoehn G]]
		+	[[Category: Van Genderen E]]

OCA at 09:28, 29 July 2020

OCA — Wed, 29 Jul 2020 09:28:17 GMT

←Older revision		Revision as of 09:28, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6zhn is ON HOLD	+	The entry 6zhn is ON HOLD until Paper Publication

	Authors: Blum, T., Housset, D., Clabbers, M.T.B., van Genderen, E., Schoehn, G., Ling, W.L., Abrahams, J.P.		Authors: Blum, T., Housset, D., Clabbers, M.T.B., van Genderen, E., Schoehn, G., Ling, W.L., Abrahams, J.P.

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

OCA — Wed, 08 Jul 2020 11:09:27 GMT

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

←Older revision

Revision as of 11:09, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zhn is ON HOLD Authors: Blum, T., Housset, D., Clabbers, M.T.B., van Genderen, E., Schoehn, G., Ling, W.L., Abrahams, J.P. Description: 3D electro...

OCA — Wed, 08 Jul 2020 11:09:26 GMT

New page: '''Unreleased structure''' The entry 6zhn is ON HOLD Authors: Blum, T., Housset, D., Clabbers, M.T.B., van Genderen, E., Schoehn, G., Ling, W.L., Abrahams, J.P. Description: 3D electro...

New page

'''Unreleased structure'''

The entry 6zhn is ON HOLD

Authors: Blum, T., Housset, D., Clabbers, M.T.B., van Genderen, E., Schoehn, G., Ling, W.L., Abrahams, J.P.

Description: 3D electron diffraction structure of thaumatin from Thaumatococcus daniellii
[[Category: Unreleased Structures]]
[[Category: Abrahams, J.P]]
[[Category: Housset, D]]
[[Category: Schoehn, G]]
[[Category: Van Genderen, E]]
[[Category: Ling, W.L]]
[[Category: Clabbers, M.T.B]]
[[Category: Blum, T]]