5d99

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<StructureSection load='5d99' size='340' side='right'caption='[[5d99]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
<StructureSection load='5d99' size='340' side='right'caption='[[5d99]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5d99]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D99 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5d99]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_L1 Enterobacteria phage L1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D99 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5d99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d99 OCA], [https://pdbe.org/5d99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d99 RCSB], [https://www.ebi.ac.uk/pdbsum/5d99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d99 ProSAT]</span></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dw4|3dw4]]</td></tr>
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<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=5d99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d99 OCA], [http://pdbe.org/5d99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d99 RCSB], [http://www.ebi.ac.uk/pdbsum/5d99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d99 ProSAT]</span></td></tr>
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</table>
</table>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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Site-specific 2'-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 2'-OCH(3)-modified RNA sequences, prior to the replacement of 2'-OCH(3) groups with their 2'-SeCH(3) counterparts. The method exploits the similar crystallization properties of 2'-OCH(3)- and 2'-SeCH(3)-modified RNAs and has been successfully validated for two test cases. In addition, our data show that 2'-SeCH(3)-modified RNA have an increased resistance to X-ray radiolysis in comparison with commonly used 5-halogen-modified RNA, which permits collection of experimental electron density maps of remarkable quality.
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Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 A) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the l Miller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. More sensitive methods are needed for the automated detection of partial TPS.
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A fast selenium derivatization strategy for crystallization and phasing of RNA structures.,Olieric V, Rieder U, Lang K, Serganov A, Schulze-Briese C, Micura R, Dumas P, Ennifar E RNA. 2009 Apr;15(4):707-15. Epub 2009 Feb 18. PMID:19228585<ref>PMID:19228585</ref>
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Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry.,Mooers BH Acta Crystallogr D Struct Biol. 2016 Apr;72(Pt 4):477-87. doi:, 10.1107/S2059798316001224. Epub 2016 Mar 24. PMID:27050127<ref>PMID:27050127</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Enterobacteria phage L1]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Mooers, B H.M]]
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[[Category: Mooers BHM]]
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[[Category: Ab initio direct methods structure determination]]
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[[Category: Hairpin rna]]
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[[Category: Rna]]
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Revision as of 10:26, 21 June 2023

3DW4 redetermined by direct methods starting from random phase angles

PDB ID 5d99

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