2pw5: Difference between revisions

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 ==Crystal Structure of Staphylococcal nuclease variant V66Y/P117G/H124L/S128A at room temperature==
-<StructureSection load='2pw5' size='340' side='right' caption='[[2pw5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2pw5' size='340' side='right'caption='[[2pw5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pw5]] 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=2PW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PW5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pw5]] 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=2PW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PW5 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u9r|1u9r]], [[2pw7|2pw7]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</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=2pw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pw5 OCA], [https://pdbe.org/2pw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pw5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pw5 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>
+</table>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pw5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pw5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pw5 PDBsum]</span></td></tr>
+== Function ==
-<table>
+[https://www.uniprot.org/uniprot/A5A520_STAAU A5A520_STAAU]
 == 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/pw/2pw5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pw/2pw5_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2pw5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Although internal water molecules are essential for the structure and function of many proteins, the structural and physical factors that govern internal hydration are poorly understood. We have examined the molecular determinants of internal hydration systematically, by solving the crystal structures of variants of staphylococcal nuclease with Gln-66, Asn-66, and Tyr-66 at cryo (100 K) and room (298 K) temperatures, and comparing them with existing cryo and room temperature structures of variants with Glu-66, Asp-66, Lys-66, Glu-92 or Lys-92 obtained under conditions of pH where the internal ionizable groups are in the neutral state. At cryogenic temperatures the polar moieties of all these internal side chains are hydrated except in the cases of Lys-66 and Lys-92. At room temperature the internal water molecules were observed only in variants with Glu-66 and Tyr-66; water molecules in the other variants are probably present but they are disordered and therefore undetectable crystallographically. Each internal water molecule establishes between 3 and 5 hydrogen bonds with the protein or with other internal water molecules. The strength of interactions between internal polar side chains and water molecules seems to decrease from carboxylic acids to amides to amines. Low temperature, low cavity volume, and the presence of oxygen atoms in the cavity increase the positional stability of internal water molecules. This set of structures and the physical insight they contribute into internal hydration will be useful for the development and benchmarking of computational methods for artificial hydration of pockets, cavities, and active sites in proteins.
-Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.,Schlessman JL, Abe C, Gittis A, Karp DA, Dolan MA, Garcia-Moreno E B Biophys J. 2008 Apr 15;94(8):3208-16. Epub 2008 Jan 4. PMID:18178652<ref>PMID:18178652</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Staphylococcal nuclease|Staphylococcal nuclease]]
+*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Micrococcal nuclease]]
+[[Category: Large Structures]]
 [[Category: Staphylococcus aureus]]
-[[Category: Abe, C.]]
+[[Category: Abe C]]
-[[Category: Garcia-Moreno, E B.]]
+[[Category: Garcia-Moreno EB]]
-[[Category: Schlessman, J L.]]
+[[Category: Schlessman JL]]
-[[Category: Hydrolase]]
-[[Category: Hyperstable variant]]
-[[Category: Internal water]]
-[[Category: Nuclease]]
-[[Category: Staphyloccal nuclease]]