1a3v: Difference between revisions

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-[[Image:1a3v.png|left|200px]]
-{{STRUCTURE_1a3v|  PDB=1a3v  |  SCENE=  }}
+==STAPHYLOCOCCAL NUCLEASE, CYCLOPENTANE THIOL DISULFIDE TO V23C VARIANT==
+<StructureSection load='1a3v' size='340' side='right'caption='[[1a3v]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1a3v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A3V 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5C:S-CYCLOPENTYL+THIOCYSTEINE'>C5C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</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=1a3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a3v OCA], [https://pdbe.org/1a3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a3v RCSB], [https://www.ebi.ac.uk/pdbsum/1a3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a3v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
+== 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/a3/1a3v_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=1a3v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined by X-ray crystallography the structures of several variants of staphylococcal nuclease with long flexible straight chain and equivalent length cyclic unnatural amino acid side chains embedded in the protein core. The terminal atoms in the straight side chains are not well defined by the observed electron density even though they remain buried within the protein interior. We have previously observed this behavior and have suggested that it may arise from the addition of side-chain vibrational and oscillational motions with each bond as a side chain grows away from the relatively rigid protein main chain and/or the population of multiple rotamers (Wynn R, Harkins P, Richards FM. Fox RO. 1996. Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci 5:1026-1031). Reduction of the number of degrees of freedom by cyclization of a side chain would be expected to constrain these motions. These side chains are in fact well defined in the structures described here. Over-packing of the protein core results in a 1.0 A shift of helix 1 away from the site of mutation. Additionally, we have determined the structure of a side chain containing a single hydrogen to fluorine atom replacement on a methyl group. A fluorine atom is intermediate in size between methyl group and a hydrogen atom. The fluorine atom is observed in a single position indicating it does not rotate like methyl hydrogen atoms. This change also causes subtle differences in the packing interactions.
-===STAPHYLOCOCCAL NUCLEASE, CYCLOPENTANE THIOL DISULFIDE TO V23C VARIANT===
+Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease.,Wynn R, Harkins PC, Richards FM, Fox RO Protein Sci. 1997 Aug;6(8):1621-6. PMID:9260275<ref>PMID:9260275</ref>
-{{ABSTRACT_PUBMED_9260275}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1a3v" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[1a3v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A3V OCA].
+*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:009260275</ref><references group="xtra"/>
+__TOC__
-[[Category: Micrococcal nuclease]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Staphylococcus aureus]]
-[[Category: Fox, R O.]]
+[[Category: Fox RO]]
-[[Category: Harkins, P C.]]
+[[Category: Harkins PC]]
-[[Category: Richards, F M.]]
+[[Category: Richards FM]]
-[[Category: Wynn, R.]]
+[[Category: Wynn R]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]
-[[Category: Unnatural amino acid]]