1tra - Revision history

OCA at 08:41, 14 February 2024

OCA — Wed, 14 Feb 2024 08:41:24 GMT

←Older revision		Revision as of 08:41, 14 February 2024
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [https://pdbe.org/1tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [https://www.ebi.ac.uk/pdbsum/1tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra 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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [https://pdbe.org/1tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [https://www.ebi.ac.uk/pdbsum/1tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of yeast phenylalanine transfer RNA in the monoclinic form has been further refined by using the restrained least-squares method of Hendrickson and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at least 3 times their standard deviations, the R factor is 16.8%. The variation of the atomic temperature factors along the sequence indicates that the major flexibility regions are the amino acid and anticodon stems. The two strands of the amino acid helix exhibit large differential temperature factors, suggesting partial uncoiling or melting of the helix. In this work, the occupancy of all atoms was also varied. Residues D16 and D17 of the dihydrouridine loop as well as U33 and G37 of the anticodon loop have occupancies around 70%, indicating some local disorder or large-scale mobility at these positions. One hundred fifteen solvent molecules, including five magnesium ions, were found in difference maps. The role of several water molecules is clearly related to the stabilization of the secondary and tertiary interactions. The gold sites, which were not previously discussed, are described and show an energetically favored binding mode similar to that of cobalt and nickel complexes with nucleotides.
-
-	Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles.,Westhof E, Sundaralingam M Biochemistry. 1986 Aug 26;25(17):4868-78. PMID:3533142<ref>PMID:3533142</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1tra" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]		*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:04, 5 July 2023

OCA — Wed, 05 Jul 2023 06:04:16 GMT

←Older revision		Revision as of 06:04, 5 July 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [https://pdbe.org/1tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [https://www.ebi.ac.uk/pdbsum/1tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra 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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [https://pdbe.org/1tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [https://www.ebi.ac.uk/pdbsum/1tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra ProSAT]</span></td></tr>
	</table>		</table>
Line 26:		Line 26:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Sundaralingam, M]]	+	[[Category: Sundaralingam M]]
-	[[Category: Westhof, E]]	+	[[Category: Westhof E]]
-	~~[[Category: Loop]]~~	+
-	~~[[Category: Single strand]]~~	+
-	~~[[Category: T-rna~~]]	+

OCA at 09:31, 29 September 2021

OCA — Wed, 29 Sep 2021 09:31:29 GMT

←Older revision		Revision as of 09:31, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='1tra' size='340' side='right'caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1tra' size='340' side='right'caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TRA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [~~http~~://pdbe.org/1tra PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tra PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra 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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [https://pdbe.org/1tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [https://www.ebi.ac.uk/pdbsum/1tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	==See Also==		==See Also==
	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]		*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
-	*[[Transfer RNA tour\|Transfer RNA tour]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:12, 25 December 2019

OCA — Wed, 25 Dec 2019 14:12:21 GMT

←Older revision		Revision as of 14:12, 25 December 2019
Line 1:		Line 1:

	==RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES==		==RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES==
-	<StructureSection load='1tra' size='340' side='right' caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1tra' size='340' side='right'caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRA FirstGlance]. <br>
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[~~TRNA~~\|~~TRNA~~]]	+	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	*[[Transfer RNA tour\|Transfer RNA tour]]		*[[Transfer RNA tour\|Transfer RNA tour]]
	== References ==		== References ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Sundaralingam, M]]		[[Category: Sundaralingam, M]]

OCA at 09:00, 21 March 2018

OCA — Wed, 21 Mar 2018 09:00:48 GMT

←Older revision		Revision as of 09:00, 21 March 2018
Line 1:		Line 1:
		+
	==RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES==		==RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES==
	<StructureSection load='1tra' size='340' side='right' caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1tra' size='340' side='right' caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [http://pdbe.org/1tra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [http://www.ebi.ac.uk/pdbsum/1tra 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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [http://pdbe.org/1tra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [http://www.ebi.ac.uk/pdbsum/1tra PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tra ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	==See Also==		==See Also==
	*[[TRNA\|TRNA]]		*[[TRNA\|TRNA]]
		+	*[[Transfer RNA tour\|Transfer RNA tour]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:08, 10 September 2015

OCA — Thu, 10 Sep 2015 08:08:09 GMT

←Older revision		Revision as of 08:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1tra' size='340' side='right' caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1tra' size='340' side='right' caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=8tna 8tna], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7tna 7tna] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [http://www.ebi.ac.uk/pdbsum/1tra 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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [http://pdbe.org/1tra PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [http://www.ebi.ac.uk/pdbsum/1tra PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 1tra" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:11, 17 December 2014

OCA — Wed, 17 Dec 2014 14:11:07 GMT

←Older revision		Revision as of 14:11, 17 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1tra\| PDB=1tra \| SCENE= }}~~	+	==RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES==
-	===RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES===	+	<StructureSection load='1tra' size='340' side='right' caption='[[1tra]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_3533142}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TRA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tra OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tra RCSB], [http://www.ebi.ac.uk/pdbsum/1tra PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structure of yeast phenylalanine transfer RNA in the monoclinic form has been further refined by using the restrained least-squares method of Hendrickson and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at least 3 times their standard deviations, the R factor is 16.8%. The variation of the atomic temperature factors along the sequence indicates that the major flexibility regions are the amino acid and anticodon stems. The two strands of the amino acid helix exhibit large differential temperature factors, suggesting partial uncoiling or melting of the helix. In this work, the occupancy of all atoms was also varied. Residues D16 and D17 of the dihydrouridine loop as well as U33 and G37 of the anticodon loop have occupancies around 70%, indicating some local disorder or large-scale mobility at these positions. One hundred fifteen solvent molecules, including five magnesium ions, were found in difference maps. The role of several water molecules is clearly related to the stabilization of the secondary and tertiary interactions. The gold sites, which were not previously discussed, are described and show an energetically favored binding mode similar to that of cobalt and nickel complexes with nucleotides.

-	~~==About this Structure==~~	+	Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles.,Westhof E, Sundaralingam M Biochemistry. 1986 Aug 26;25(17):4868-78. PMID:3533142<ref>PMID:3533142</ref>
-	~~[[1tra]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~This structure supersedes the now removed PDB entries and [http~~:~~//oca.weizmann.ac.il/oca~~-~~bin/send-pdb?obs=1&id=2tna 2tna]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1TRA OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[TRNA\|TRNA]]		*[[TRNA\|TRNA]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:003533142<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Sundaralingam, M.]]	+	[[Category: Sundaralingam, M]]
-	[[Category: Westhof, E.]]	+	[[Category: Westhof, E]]
	[[Category: Loop]]		[[Category: Loop]]
	[[Category: Single strand]]		[[Category: Single strand]]
	[[Category: T-rna]]		[[Category: T-rna]]

OCA at 10:08, 11 March 2013

OCA — Mon, 11 Mar 2013 10:08:44 GMT

←Older revision		Revision as of 10:08, 11 March 2013
Line 1:		Line 1:
-	[[Image:1tra.png\|left\|200px]]
-
	{{STRUCTURE_1tra\| PDB=1tra \| SCENE= }}		{{STRUCTURE_1tra\| PDB=1tra \| SCENE= }}
-
	===RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES===		===RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES===
-
	{{ABSTRACT_PUBMED_3533142}}		{{ABSTRACT_PUBMED_3533142}}

OCA at 09:00, 20 October 2012

OCA — Sat, 20 Oct 2012 09:00:17 GMT

←Older revision		Revision as of 09:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1tra]] is a 1 chain structure ~~of [[TRNA]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA].	+	[[1tra]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tna 2tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TRA OCA].

	==See Also==		==See Also==

OCA at 21:28, 25 July 2012

OCA — Wed, 25 Jul 2012 21:28:02 GMT

←Older revision		Revision as of 21:28, 25 July 2012
Line 1:		Line 1:
	[[Image:1tra.png\|left\|200px]]		[[Image:1tra.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1tra\| PDB=1tra \| SCENE= }}		{{STRUCTURE_1tra\| PDB=1tra \| SCENE= }}

	===RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES===		===RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES===

-
-	<!--
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	{{ABSTRACT_PUBMED_3533142}}		{{ABSTRACT_PUBMED_3533142}}

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	==See Also==		==See Also==
-	*[[TRNA]]	+	*[[TRNA\|TRNA]]

	==Reference==		==Reference==