6dpp - Revision history

OCA at 06:12, 11 October 2023

2023-10-11T06:12:21Z

←Older revision		Revision as of 06:12, 11 October 2023
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	<StructureSection load='6dpp' size='340' side='right'caption='[[6dpp]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6dpp' size='340' side='right'caption='[[6dpp]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dpp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dpp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DPP FirstGlance]. <br>
-	</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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.45Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></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=6dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpp OCA], [~~http~~://pdbe.org/6dpp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dpp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dpp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpp 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=6dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpp OCA], [https://pdbe.org/6dpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dpp RCSB], [https://www.ebi.ac.uk/pdbsum/6dpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RNH1_BACHD RNH1_BACHD]~~] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	+	[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alkalihalobacillus halodurans C-125]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ribonuclease H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Samara~~, N L~~]]	+	[[Category: Samara NL]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	~~[[Category: Divalent cation]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Hydrolase-rna-dna complex]]~~	+
-	~~[[Category: In crystallo catalysis]]~~	+
-	~~[[Category: Metal dependent catalysis]]~~	+
-	~~[[Category: Monovalent cation]]~~	+
-	~~[[Category: Protein-rna-dna complex]]~~	+
-	~~[[Category: Rna hydrolysis~~]]	+

OCA at 09:07, 11 November 2020

2020-11-11T09:07:36Z

←Older revision		Revision as of 09:07, 11 November 2020
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	==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C==		==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C==
-	<StructureSection load='6dpp' size='340' side='right' caption='[[6dpp]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='6dpp' size='340' side='right'caption='[[6dpp]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dpp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dpp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DPP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>	+	</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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=6dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpp OCA], [http://pdbe.org/6dpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dpp RCSB], [http://www.ebi.ac.uk/pdbsum/6dpp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpp 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=6dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpp OCA], [http://pdbe.org/6dpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dpp RCSB], [http://www.ebi.ac.uk/pdbsum/6dpp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 6dpp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dpp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Samara, N L]]		[[Category: Samara, N L]]

OCA at 16:19, 15 August 2018

2018-08-15T16:19:57Z

←Older revision		Revision as of 16:19, 15 August 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6dpp is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C==
		+	<StructureSection load='6dpp' size='340' side='right' caption='[[6dpp]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dpp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DPP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </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=6dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpp OCA], [http://pdbe.org/6dpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dpp RCSB], [http://www.ebi.ac.uk/pdbsum/6dpp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg(2+) ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg(2+) ions and an additional K(+) failed to align the nucleophilic water for RNA cleavage. Substrate alignment and product formation required a second K(+) and a third Mg(2+), which replaced the first K(+) and departed immediately after cleavage. A third transient Mg(2+) has also been observed for DNA synthesis, but in that case it coordinates the leaving group instead of the nucleophile as in the case of the RNase H1 hydrolysis reaction. These transient cations have no contact with the enzymes. Other DNA and RNA enzymes that catalyze consecutive cleavage and strand-transfer reactions in a single active site may similarly require cation trafficking coordinated by the substrate.

-	~~Authors:~~ Samara, N.L., ~~Yang, W~~.	+	Cation trafficking propels RNA hydrolysis.,Samara NL, Yang W Nat Struct Mol Biol. 2018 Aug;25(8):715-721. doi: 10.1038/s41594-018-0099-4. Epub, 2018 Aug 3. PMID:30076410<ref>PMID:30076410</ref>

-	~~Description: Crystal Structure~~ of ~~Bacillus Halodurans Ribonuclease H1 in Complex with an RNA~~/~~DNA Hybrid~~: ~~Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Samara, N.L]]	+	<div class="pdbe-citations 6dpp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribonuclease H]]
		+	[[Category: Samara, N L]]
	[[Category: Yang, W]]		[[Category: Yang, W]]
		+	[[Category: Divalent cation]]
		+	[[Category: Double helix]]
		+	[[Category: Hydrolase-rna-dna complex]]
		+	[[Category: In crystallo catalysis]]
		+	[[Category: Metal dependent catalysis]]
		+	[[Category: Monovalent cation]]
		+	[[Category: Protein-rna-dna complex]]
		+	[[Category: Rna hydrolysis]]

OCA at 05:48, 25 July 2018

2018-07-25T05:48:29Z

←Older revision		Revision as of 05:48, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Samara, N.L., Yang, W.		Authors: Samara, N.L., Yang, W.

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

2018-06-20T04:06:08Z

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

←Older revision

Revision as of 04:06, 20 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dpp is ON HOLD Authors: Samara, N.L., Yang, W. Description: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hy...

2018-06-20T04:06:07Z

New page: '''Unreleased structure''' The entry 6dpp is ON HOLD Authors: Samara, N.L., Yang, W. Description: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hy...

New page

'''Unreleased structure'''

The entry 6dpp is ON HOLD

Authors: Samara, N.L., Yang, W.

Description: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C
[[Category: Unreleased Structures]]
[[Category: Samara, N.L]]
[[Category: Yang, W]]