1nkw: Difference between revisions

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-[[Image:1nkw.png|left|200px]]
-{{STRUCTURE_1nkw|  PDB=1nkw  |  SCENE=  }}
+==Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans==
+<StructureSection load='1nkw' size='340' side='right'caption='[[1nkw]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nkw]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lnr 1lnr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kpj 1kpj] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc9 1kc9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKW FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</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=1nkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkw OCA], [https://pdbe.org/1nkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkw RCSB], [https://www.ebi.ac.uk/pdbsum/1nkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL2_DEIRA RL2_DEIRA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_B]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nkw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.
-===Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans===
+High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.,Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A Cell. 2001 Nov 30;107(5):679-88. PMID:11733066<ref>PMID:11733066</ref>
-{{ABSTRACT_PUBMED_11733066}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1nkw" style="background-color:#fffaf0;"></div>
-[[1nkw]] is a 30 chain structure of [[Kink-turn motif]], [[Large Ribosomal Subunit of Haloarcula]], [[Ribosomal protein L11]], [[Ribosomal protein L13]], [[Ribosomal protein L14]], [[Ribosomal protein L15]], [[Ribosomal protein L16]], [[Ribosomal protein L17]], [[Ribosomal protein L18]], [[Ribosomal protein L19]], [[Ribosomal protein L2]], [[Ribosomal protein L20]], [[Ribosomal protein L21]], [[Ribosomal protein L22]], [[Ribosomal protein L23]], [[Ribosomal protein L24]], [[Ribosomal protein L27]], [[Ribosomal protein L29]], [[Ribosomal protein L3]], [[Ribosomal protein L30]], [[Ribosomal protein L31]], [[Ribosomal protein L32]], [[Ribosomal protein L33]], [[Ribosomal protein L34]], [[Ribosomal protein L35]], [[Ribosomal protein L36]], [[Ribosomal protein L4]], [[Ribosomal protein L5]], [[Ribosomal protein L6]], [[Ribosomal protein L9]], [[Ribosome]] and [[User:Wayne Decatur/kink-turn motif]] with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc9 1kc9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKW OCA].
 ==See Also==
 *[[Kink-turn motif|Kink-turn motif]]
 *[[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit of Haloarcula]]
-*[[Ribosomal protein L11|Ribosomal protein L11]]
-*[[Ribosomal protein L13|Ribosomal protein L13]]
-*[[Ribosomal protein L14|Ribosomal protein L14]]
-*[[Ribosomal protein L15|Ribosomal protein L15]]
-*[[Ribosomal protein L16|Ribosomal protein L16]]
-*[[Ribosomal protein L17|Ribosomal protein L17]]
-*[[Ribosomal protein L18|Ribosomal protein L18]]
-*[[Ribosomal protein L19|Ribosomal protein L19]]
-*[[Ribosomal protein L2|Ribosomal protein L2]]
-*[[Ribosomal protein L20|Ribosomal protein L20]]
-*[[Ribosomal protein L21|Ribosomal protein L21]]
-*[[Ribosomal protein L22|Ribosomal protein L22]]
-*[[Ribosomal protein L23|Ribosomal protein L23]]
-*[[Ribosomal protein L24|Ribosomal protein L24]]
-*[[Ribosomal protein L27|Ribosomal protein L27]]
-*[[Ribosomal protein L29|Ribosomal protein L29]]
-*[[Ribosomal protein L3|Ribosomal protein L3]]
-*[[Ribosomal protein L30|Ribosomal protein L30]]
-*[[Ribosomal protein L31|Ribosomal protein L31]]
-*[[Ribosomal protein L32|Ribosomal protein L32]]
-*[[Ribosomal protein L33|Ribosomal protein L33]]
-*[[Ribosomal protein L34|Ribosomal protein L34]]
-*[[Ribosomal protein L35|Ribosomal protein L35]]
-*[[Ribosomal protein L36|Ribosomal protein L36]]
-*[[Ribosomal protein L4|Ribosomal protein L4]]
-*[[Ribosomal protein L5|Ribosomal protein L5]]
-*[[Ribosomal protein L6|Ribosomal protein L6]]
-*[[Ribosomal protein L9|Ribosomal protein L9]]
 *[[Ribosome|Ribosome]]
-*[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit|User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
 *[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:011733066</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Agmon, I.]]
+[[Category: Large Structures]]
-[[Category: Bartels, H.]]
+[[Category: Agmon I]]
-[[Category: Bashan, A.]]
+[[Category: Bartels H]]
-[[Category: Franceschi, F.]]
+[[Category: Bashan A]]
-[[Category: Gat, S.]]
+[[Category: Franceschi F]]
-[[Category: Harms, J M.]]
+[[Category: Gat S]]
-[[Category: Schluenzen, F.]]
+[[Category: Harms JM]]
-[[Category: Yonath, A.]]
+[[Category: Schluenzen F]]
-[[Category: Zarivach, R.]]
+[[Category: Yonath A]]
-[[Category: 50]]
+[[Category: Zarivach R]]
-[[Category: Deinococcus radioduran]]
-[[Category: Large subunit]]
-[[Category: Peptide bond formation]]
-[[Category: Peptidyl-transferase]]
-[[Category: Ribosome]]
-[[Category: X-ray structure]]