1g4q - Revision history

OCA at 07:22, 7 February 2024

OCA — Wed, 07 Feb 2024 07:22:50 GMT

←Older revision		Revision as of 07:22, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
-	</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.15Å</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [https://pdbe.org/1g4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [https://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4q 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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [https://pdbe.org/1g4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [https://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4q ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.
-
-	Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution.,Han GW Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466<ref>PMID:11173466</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1g4q" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Han GW]]		[[Category: Han GW]]

OCA at 09:33, 28 December 2022

OCA — Wed, 28 Dec 2022 09:33:11 GMT

←Older revision		Revision as of 09:33, 28 December 2022
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Han~~, G W]]~~	+	[[Category: Han GW]]
-	~~[[Category: Direct method]]~~	+
-	~~[[Category: Dna-rna complex]]~~	+
-	~~[[Category: Dna-rna hybrid]]~~	+
-	~~[[Category: Polypurine tract of hiv-1]]~~	+
-	~~[[Category: Rna/dna hybrid~~]]	+

OCA at 07:11, 24 March 2021

OCA — Wed, 24 Mar 2021 07:11:36 GMT

←Older revision		Revision as of 07:11, 24 March 2021
Line 3:		Line 3:
	<StructureSection load='1g4q' size='340' side='right'caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='1g4q' size='340' side='right'caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>	+	</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [~~http~~://pdbe.org/1g4q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4q 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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [https://pdbe.org/1g4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [https://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4q ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:11, 19 June 2019

OCA — Wed, 19 Jun 2019 07:11:36 GMT

←Older revision		Revision as of 07:11, 19 June 2019
Line 1:		Line 1:

	==RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG==		==RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG==
-	<StructureSection load='1g4q' size='340' side='right' caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>	+	<StructureSection load='1g4q' size='340' side='right'caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Han, G W]]		[[Category: Han, G W]]
	[[Category: Direct method]]		[[Category: Direct method]]

OCA at 11:00, 13 September 2017

OCA — Wed, 13 Sep 2017 11:00:09 GMT

←Older revision		Revision as of 11:00, 13 September 2017
Line 1:		Line 1:
		+
	==RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG==		==RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG==
	<StructureSection load='1g4q' size='340' side='right' caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='1g4q' size='340' side='right' caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [http://pdbe.org/1g4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [http://www.ebi.ac.uk/pdbsum/1g4q PDBsum]</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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [http://pdbe.org/1g4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [http://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4q ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:23, 10 September 2015

OCA — Thu, 10 Sep 2015 19:23:53 GMT

←Older revision		Revision as of 19:23, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [http://www.ebi.ac.uk/pdbsum/1g4q PDBsum]</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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [http://pdbe.org/1g4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [http://www.ebi.ac.uk/pdbsum/1g4q PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1g4q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:05, 22 December 2014

OCA — Mon, 22 Dec 2014 22:05:45 GMT

←Older revision		Revision as of 22:05, 22 December 2014
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Han, G W.]]	+	[[Category: Han, G W]]
	[[Category: Direct method]]		[[Category: Direct method]]
	[[Category: Dna-rna complex]]		[[Category: Dna-rna complex]]

OCA at 11:34, 20 October 2014

OCA — Mon, 20 Oct 2014 11:34:56 GMT

←Older revision		Revision as of 11:34, 20 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1g4q.~~png~~\|~~left\|200px~~]]	+	==RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG==
		+	<StructureSection load='1g4q' size='340' side='right' caption='[[1g4q]], [[Resolution\|resolution]] 1.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [http://www.ebi.ac.uk/pdbsum/1g4q PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.

-	~~{{STRUCTURE_1g4q\| PDB=1g4q \| SCENE= }}~~	+	Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution.,Han GW Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466<ref>PMID:11173466</ref>

-	~~===RNA~~/~~DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11173466}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1g4q]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1G4Q OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011173466<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Han, G W.]]		[[Category: Han, G W.]]
	[[Category: Direct method]]		[[Category: Direct method]]

OCA at 09:53, 16 January 2013

OCA — Wed, 16 Jan 2013 09:53:24 GMT

←Older revision		Revision as of 09:53, 16 January 2013
Line 1:		Line 1:
	[[Image:1g4q.png\|left\|200px]]		[[Image:1g4q.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1g4q", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1g4q\| PDB=1g4q \| SCENE= }}		{{STRUCTURE_1g4q\| PDB=1g4q \| SCENE= }}

	===RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG===		===RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11173466}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11173466 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11173466}}		{{ABSTRACT_PUBMED_11173466}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11173466</ref><ref group="xtra">PMID:14636594~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011173466</ref><references group="xtra"/>
	[[Category: Han, G W.]]		[[Category: Han, G W.]]
	[[Category: Direct method]]		[[Category: Direct method]]
		+	[[Category: Dna-rna complex]]
	[[Category: Dna-rna hybrid]]		[[Category: Dna-rna hybrid]]
-	[[Category: Dna/rna complex]]
	[[Category: Polypurine tract of hiv-1]]		[[Category: Polypurine tract of hiv-1]]
	[[Category: Rna/dna hybrid]]		[[Category: Rna/dna hybrid]]

OCA: Protected "1g4q" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 18:38:47 GMT

Protected "1g4q" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:38, 14 March 2011