3tra: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3tra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=9tna 9tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TRA FirstGlance]. <br>
<table><tr><td colspan='2'>[[3tra]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=9tna 9tna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TRA 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]] 3&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=3tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tra OCA], [https://pdbe.org/3tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tra RCSB], [https://www.ebi.ac.uk/pdbsum/3tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tra 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=3tra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tra OCA], [https://pdbe.org/3tra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tra RCSB], [https://www.ebi.ac.uk/pdbsum/3tra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tra ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% for about 4500 reflections between 10 and 3 A. In yeast tRNA(Asp) crystals the molecules exist as dimers with base pairings of the anticodon (AC) triplets and labilization of the tertiary interaction between one invariant guanine of the dihydrouridine (D) loop and the invariant cytosine of the thymine (T) loop (G19-C56). In yeast tRNA(Phe) crystals, the molecules exist as monomers with only weak intermolecular packing contacts between symmetry-related molecules. Despite this, the tertiary folds of the L-shaped tRNA structures are identical when allowance is made for base sequence changes between tRNA(Phe) and tRNA(Asp). However, the relative mobilities of two regions are inverse in the two structures with the AC loop more mobile than the D loop in tRNA(Phe) and the D loop more mobile than the AC loop in tRNA(Asp). In addition, the T loop becomes mobile in tRNA(Asp). The present refinements were performed to exclude packing effects or refinement bias as possible sources of such differential dynamic behavior. It is concluded that the transfer of flexibility from the anticodon to the D- and T-loop region in tRNA(Asp) is not a crystal-line artefact. Further, analysis of the four structures supports a mechanism for the flexibility transfer through base stacking in the AC loop and concomitant variations in twist angles between base pairs of the anticodon helix which propagate up to the D- and T-loop region.
Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.,Westhof E, Dumas P, Moras D Acta Crystallogr A. 1988 Mar 1;44 ( Pt 2):112-23. PMID:3272146<ref>PMID:3272146</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3tra" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Dumas, P]]
[[Category: Dumas P]]
[[Category: Moras, D]]
[[Category: Moras D]]
[[Category: Westhof, E]]
[[Category: Westhof E]]
[[Category: Loop]]
[[Category: Single strand]]
[[Category: T-rna]]

Latest revision as of 13:10, 1 March 2024

RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALSRESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS

Structural highlights

3tra is a 1 chain structure with sequence from Saccharomyces cerevisiae. This structure supersedes the now removed PDB entry 9tna. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

3tra, resolution 3.00Å

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OCA
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