2gq7: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2gq7.gif|left|200px]]


<!--
==Crystal structure of an RNA racemate==
The line below this paragraph, containing "STRUCTURE_2gq7", creates the "Structure Box" on the page.
<StructureSection load='2gq7' size='340' side='right'caption='[[2gq7]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2gq7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GQ7 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-->
<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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
{{STRUCTURE_2gq7|  PDB=2gq7  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gq7 OCA], [https://pdbe.org/2gq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gq7 RCSB], [https://www.ebi.ac.uk/pdbsum/2gq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gq7 ProSAT]</span></td></tr>
 
</table>
'''Crystal structure of an RNA racemate'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Betzel C]]
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.
[[Category: Erdmann VA]]
 
[[Category: Klussmann S]]
==About this Structure==
[[Category: Perbandt M]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ7 OCA].  
[[Category: Rypniewski W]]
 
[[Category: Vallazza M]]
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/16699193 16699193]
[[Category: Betzel, C.]]
[[Category: Erdmann, V A.]]
[[Category: Klussmann, S.]]
[[Category: Perbandt, M.]]
[[Category: Rypniewski, W.]]
[[Category: Vallazza, M.]]
[[Category: Double helix]]
[[Category: Racemate]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 05:23:45 2008''

Latest revision as of 12:29, 14 February 2024

Crystal structure of an RNA racemateCrystal structure of an RNA racemate

Structural highlights

2gq7 is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

2gq7, resolution 1.60Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2gq7&oldid=4058786"