6zhj - Revision history

OCA at 16:03, 14 March 2024

2024-03-14T16:03:56Z

←Older revision		Revision as of 16:03, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.		[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
-	<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 6zhj" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:49, 24 January 2024

2024-01-24T13:49:47Z

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

	==3D electron diffraction structure of thermolysin from Bacillus thermoproteolyticus==		==3D electron diffraction structure of thermolysin from Bacillus thermoproteolyticus==
-	<StructureSection load='6zhj' size='340' side='right'caption='[[6zhj]]' scene=''>	+	<StructureSection load='6zhj' size='340' side='right'caption='[[6zhj]], [[Resolution\|resolution]] 3.26Å' 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=6ZHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zhj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHJ 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=6zhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhj OCA], [https://pdbe.org/6zhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhj RCSB], [https://www.ebi.ac.uk/pdbsum/6zhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhj 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]] 3.26Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6zhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhj OCA], [https://pdbe.org/6zhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhj RCSB], [https://www.ebi.ac.uk/pdbsum/6zhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
		+	<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 6zhj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus thermoproteolyticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Abrahams JP]]		[[Category: Abrahams JP]]

OCA at 07:55, 27 January 2021

2021-01-27T07:55:54Z

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

-	~~The entry~~ 6zhj ~~is ON HOLD until Paper Publication~~	+	==3D electron diffraction structure of thermolysin from Bacillus thermoproteolyticus==
-		+	<StructureSection load='6zhj' size='340' side='right'caption='[[6zhj]]' 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=6ZHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHJ FirstGlance]. <br>
-	~~Description: 3D electron diffraction structure of thermolysin from Bacillus thermoproteolyticus~~	+	</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=6zhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhj OCA], [https://pdbe.org/6zhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhj RCSB], [https://www.ebi.ac.uk/pdbsum/6zhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhj 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

2020-07-29T09:28:11Z

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

-	The entry 6zhj is ON HOLD	+	The entry 6zhj 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 "6zhj" [edit=sysop:move=sysop]

2020-07-08T11:09:08Z

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

←Older revision

Revision as of 11:09, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zhj 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...

2020-07-08T11:09:07Z

New page: '''Unreleased structure''' The entry 6zhj 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 6zhj 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 thermolysin from Bacillus thermoproteolyticus
[[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]]