2gpm

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[[Image:2gpm.gif|left|200px]]<br /><applet load="2gpm" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gpm, resolution 1.4&Aring;" />
 
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'''Crystal structure of an RNA racemate'''<br />
 
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==Overview==
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==Crystal structure of an RNA racemate==
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The racemate of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) from Thermus flavus 5S rRNA has been crystallized and examined by X-ray crystallography. The space group is P1(_) with approximate unit-cell parameters a = 26.5, b = 38.0, c = 45.4 Angstrom, alpha = 113.1, beta = 100.5, gamma = 93.3 degrees. The structure was solved by molecular replacement. There are four RNA duplexes in the unit cell. The crystal lattice consists of columns of RNA duplexes. The duplexes are stacked end-to-end and are stabilized by intermolecular base-stacking interactions. Within each column the L-duplexes and D-duplexes are stacked alternately. Every other duplex in each stack has two alternative conformations, approximately equally occupied, corresponding to molecules oriented in opposite directions. Neighbouring columns are related by the crystallographic centre of symmetry. The unit cell also contains approximately 250 ordered water molecules and six ordered calcium ions. A glycerol molecule is visible in the minor groove interacting with a guanosine residue.
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<StructureSection load='2gpm' size='340' side='right'caption='[[2gpm]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2gpm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GPM FirstGlance]. <br>
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2GPM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GPM OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0C:L-CYTIDINE-5-MONOPHOSPHATE'>0C</scene>, <scene name='pdbligand=0G:L-GUANOSINE-5-MONOPHOSPHATE'>0G</scene>, <scene name='pdbligand=0U:L-URIDINE-5-MONOPHOSPHATE'>0U</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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==Reference==
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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=2gpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gpm OCA], [https://pdbe.org/2gpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gpm RCSB], [https://www.ebi.ac.uk/pdbsum/2gpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gpm ProSAT]</span></td></tr>
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The first crystal structure of an RNA racemate., Rypniewski W, Vallazza M, Perbandt M, Klussmann S, Delucas LJ, Betzel C, Erdmann VA, Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):659-64. Epub 2006, May 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16699193 16699193]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Betzel, C.]]
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</StructureSection>
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[[Category: Erdmann, V. A.]]
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[[Category: Large Structures]]
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[[Category: Klussmann, S.]]
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[[Category: Betzel C]]
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[[Category: Perbandt, M.]]
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[[Category: Erdmann VA]]
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[[Category: Rypniewski, W.]]
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[[Category: Klussmann S]]
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[[Category: Vallazza, M.]]
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[[Category: Perbandt M]]
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[[Category: CA]]
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[[Category: Rypniewski W]]
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[[Category: double helix]]
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[[Category: Vallazza M]]
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[[Category: racemate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:33:59 2008''
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Current revision

Crystal structure of an RNA racemate

PDB ID 2gpm

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