7mdi - Revision history

OCA at 19:39, 29 May 2024

2024-05-29T19:39:18Z

←Older revision		Revision as of 19:39, 29 May 2024
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-	====	+	==Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state==
-	<StructureSection load='7mdi' size='340' side='right'caption='[[7mdi]]' scene=''>	+	<StructureSection load='7mdi' size='340' side='right'caption='[[7mdi]], [[Resolution\|resolution]] 4.30Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mdi]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae_FA_1090 Neisseria gonorrhoeae FA 1090]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MDI 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=7mdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mdi OCA], [https://pdbe.org/7mdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mdi RCSB], [https://www.ebi.ac.uk/pdbsum/7mdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mdi ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 4.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7mdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mdi OCA], [https://pdbe.org/7mdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mdi RCSB], [https://www.ebi.ac.uk/pdbsum/7mdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mdi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5F8Z6_NEIG1 Q5F8Z6_NEIG1] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides and is a promising antibiotic target, but few RNRs have been structurally characterized. We present the use of the chameleon, a commercially-available piezoelectric cryogenic electron microscopy plunger, to address complex denaturation in the Neisseria gonorrhoeae class Ia RNR. Here, we characterize the extent of denaturation of the ring-shaped complex following grid preparation using a traditional plunger and using a chameleon with varying dispense-to-plunge times. We also characterize how dispense-to-plunge time influences the amount of protein sample required for grid preparation and preferred orientation of the sample. We demonstrate that the fastest dispense-to-plunge time of 54 ms is sufficient for generation of a data set that produces a high quality structure, and that a traditional plunging technique or slow chameleon dispense-to-plunge times generate data sets limited in resolution by complex denaturation. The 4.3 A resolution structure of Neisseria gonorrhoeae class Ia RNR in the inactive alpha4beta4 oligomeric state solved using the chameleon with a fast dispense-to-plunge time yields molecular information regarding similarities and differences to the well studied Escherichia coli class Ia RNR alpha4beta4 ring.
		+
		+	Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex.,Levitz TS, Brignole EJ, Fong I, Darrow MC, Drennan CL J Struct Biol. 2022 Mar;214(1):107825. doi: 10.1016/j.jsb.2021.107825. Epub 2021 , Dec 11. PMID:34906669<ref>PMID:34906669</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mdi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Neisseria gonorrhoeae FA 1090]]
		+	[[Category: Brignole EJ]]
		+	[[Category: Drennan CL]]
		+	[[Category: Levitz TS]]

OCA at 10:40, 5 January 2022

2022-01-05T10:40:34Z

←Older revision		Revision as of 10:40, 5 January 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7mdi ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7mdi' size='340' side='right'caption='[[7mdi]]' scene=''>
-	~~Authors~~: ~~Levitz, T~~.S.~~, Drennan, C~~.L.~~, Brignole, E~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state~~	+	</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=7mdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mdi OCA], [https://pdbe.org/7mdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mdi RCSB], [https://www.ebi.ac.uk/pdbsum/7mdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mdi ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Brignole~~, E.J]]	+	__TOC__
-	[[Category: ~~Drennan, C.L~~]]	+	</StructureSection>
-	[[Category: ~~Levitz, T.S~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 02:26, 2 July 2021

2021-07-02T02:26:58Z

←Older revision		Revision as of 02:26, 2 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.		Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.
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	Description: Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state		Description: Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Brignole, E.J]]
	[[Category: Drennan, C.L]]		[[Category: Drennan, C.L]]
	[[Category: Levitz, T.S]]		[[Category: Levitz, T.S]]
-	[[Category: Brignole, E.J]]

OCA at 13:27, 2 June 2021

2021-06-02T13:27:15Z

←Older revision		Revision as of 13:27, 2 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mdi is ON HOLD ~~until Paper Publication~~	+	The entry 7mdi is ON HOLD

	Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.		Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.

OCA at 08:51, 19 May 2021

2021-05-19T08:51:28Z

←Older revision		Revision as of 08:51, 19 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.		Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.

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

2021-04-14T05:41:57Z

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

←Older revision

Revision as of 05:41, 14 April 2021

OCA: New page: '''Unreleased structure''' The entry 7mdi is ON HOLD Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J. Description: Structure of the Neisseria gonorrhoeae ribonucleotide reductase i...

2021-04-14T05:41:56Z

New page: '''Unreleased structure''' The entry 7mdi is ON HOLD Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J. Description: Structure of the Neisseria gonorrhoeae ribonucleotide reductase i...

New page

'''Unreleased structure'''

The entry 7mdi is ON HOLD

Authors: Levitz, T.S., Drennan, C.L., Brignole, E.J.

Description: Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state
[[Category: Unreleased Structures]]
[[Category: Drennan, C.L]]
[[Category: Levitz, T.S]]
[[Category: Brignole, E.J]]