7jor - Revision history

OCA at 07:16, 3 April 2024

OCA — Wed, 03 Apr 2024 07:16:42 GMT

←Older revision		Revision as of 07:16, 3 April 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]		[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.
-
-	Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.,Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Srajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA IUCrJ. 2022 Jul 25;9(Pt 5):610-624. doi: 10.1107/S2052252522006418. eCollection, 2022 Sep 1. PMID:36071813<ref>PMID:36071813</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7jor" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]		*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:30, 20 December 2023

OCA — Wed, 20 Dec 2023 12:30:34 GMT

←Older revision		Revision as of 12:30, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7jor]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JOR FirstGlance]. <br>		<table><tr><td colspan='2'>[[7jor]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JOR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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]] 2.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=7jor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jor OCA], [https://pdbe.org/7jor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jor RCSB], [https://www.ebi.ac.uk/pdbsum/7jor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jor 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=7jor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jor OCA], [https://pdbe.org/7jor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jor RCSB], [https://www.ebi.ac.uk/pdbsum/7jor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jor ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7jor" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7jor" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:42, 9 November 2022

OCA — Wed, 09 Nov 2022 07:42:41 GMT

←Older revision		Revision as of 07:42, 9 November 2022
Line 1:		Line 1:

	==Neutron structure of ferric Dehaloperoxidase B==		==Neutron structure of ferric Dehaloperoxidase B==
-	<StructureSection load='7jor' size='340' side='right'caption='[[7jor]]' scene=''>	+	<StructureSection load='7jor' size='340' side='right'caption='[[7jor]], [[Resolution\|resolution]] 2.05Å' 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=7JOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JOR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jor]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JOR 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=7jor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jor OCA], [https://pdbe.org/7jor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jor RCSB], [https://www.ebi.ac.uk/pdbsum/7jor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jor ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=7jor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jor OCA], [https://pdbe.org/7jor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jor RCSB], [https://www.ebi.ac.uk/pdbsum/7jor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jor ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.
		+
		+	Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.,Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Srajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA IUCrJ. 2022 Jul 25;9(Pt 5):610-624. doi: 10.1107/S2052252522006418. eCollection, 2022 Sep 1. PMID:36071813<ref>PMID:36071813</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jor" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Carey LM]]		[[Category: Carey LM]]

OCA at 08:57, 8 September 2021

OCA — Wed, 08 Sep 2021 08:57:10 GMT

←Older revision		Revision as of 08:57, 8 September 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7jor ~~is ON HOLD until Paper Publication~~	+	==Neutron structure of ferric Dehaloperoxidase B==
-		+	<StructureSection load='7jor' size='340' side='right'caption='[[7jor]]' scene=''>
-	~~Authors~~: ~~Carey, L~~.M., ~~Ghiladi, R~~.A., ~~Meilleur~~, F., ~~Myles, D~~.A.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JOR FirstGlance]. <br>
-	~~Description: Neutron structure of ferric Dehaloperoxidase B~~	+	</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=7jor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jor OCA], [https://pdbe.org/7jor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jor RCSB], [https://www.ebi.ac.uk/pdbsum/7jor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jor ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Meilleur, F~~]]	+	__TOC__
-	[[Category: Ghiladi~~, R.A~~]]	+	</StructureSection>
-	[[Category: ~~Myles, D.A.A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Carey, L.M~~]]	+	[[Category: Carey LM]]
		+	[[Category: Ghiladi RA]]
		+	[[Category: Meilleur F]]
		+	[[Category: Myles DAA]]

OCA at 04:14, 14 October 2020

OCA — Wed, 14 Oct 2020 04:14:33 GMT

←Older revision		Revision as of 04:14, 14 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Carey, L.M., Ghiladi, R.A., Meilleur, F., Myles, D.A.A.		Authors: Carey, L.M., Ghiladi, R.A., Meilleur, F., Myles, D.A.A.

-	Description: ~~neutron~~ structure of ferric Dehaloperoxidase B	+	Description: Neutron structure of ferric Dehaloperoxidase B
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Meilleur, F]]		[[Category: Meilleur, F]]

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

OCA — Wed, 19 Aug 2020 04:49:57 GMT

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

←Older revision

Revision as of 04:49, 19 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jor is ON HOLD Authors: Carey, L.M., Ghiladi, R.A., Meilleur, F., Myles, D.A.A. Description: neutron structure of ferric Dehaloperoxidase B [[Cate...

OCA — Wed, 19 Aug 2020 04:49:55 GMT

New page: '''Unreleased structure''' The entry 7jor is ON HOLD Authors: Carey, L.M., Ghiladi, R.A., Meilleur, F., Myles, D.A.A. Description: neutron structure of ferric Dehaloperoxidase B [[Cate...

New page

'''Unreleased structure'''

The entry 7jor is ON HOLD

Authors: Carey, L.M., Ghiladi, R.A., Meilleur, F., Myles, D.A.A.

Description: neutron structure of ferric Dehaloperoxidase B
[[Category: Unreleased Structures]]
[[Category: Meilleur, F]]
[[Category: Ghiladi, R.A]]
[[Category: Myles, D.A.A]]
[[Category: Carey, L.M]]