2oxp

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[[Image:2oxp.gif|left|200px]]
 
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==Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A==
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The line below this paragraph, containing "STRUCTURE_2oxp", creates the "Structure Box" on the page.
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<StructureSection load='2oxp' size='340' side='right'caption='[[2oxp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2oxp]] 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=2OXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXP FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2&#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=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
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{{STRUCTURE_2oxp| PDB=2oxp | SCENE= }}
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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=2oxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxp OCA], [https://pdbe.org/2oxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxp RCSB], [https://www.ebi.ac.uk/pdbsum/2oxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NUC_STAAW NUC_STAAW] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ox/2oxp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2oxp ConSurf].
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<div style="clear:both"></div>
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'''Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A'''
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==See Also==
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*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The dielectric properties of proteins are poorly understood and difficult to describe quantitatively. This limits the accuracy of methods for structure-based calculation of electrostatic energies and pK(a) values. The pK(a) values of many internal groups report apparent protein dielectric constants of 10 or higher. These values are substantially higher than the dielectric constants of 2-4 measured experimentally with dry proteins. The structural origins of these high apparent dielectric constants are not well understood. Here we report on structural and equilibrium thermodynamic studies of the effects of pH on the V66D variant of staphylococcal nuclease. In a crystal structure of this protein the neutral side chain of Asp-66 is buried in the hydrophobic core of the protein and hydrated by internal water molecules. Asp-66 titrates with a pK(a) value near 9. A decrease in the far UV-CD signal was observed, concomitant with ionization of this aspartic acid, and consistent with the loss of 1.5 turns of alpha-helix. These data suggest that the protein dielectric constant needed to reproduce the pK(a) value of Asp-66 with continuum electrostatics calculations is high because the dielectric constant has to capture, implicitly, the energetic consequences of the structural reorganization that are not treated explicitly in continuum calculations with static structures.
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[[Category: Large Structures]]
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==About this Structure==
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2OXP is a [[Single protein]] structure of 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=2OXP OCA].
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==Reference==
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High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp., Karp DA, Gittis AG, Stahley MR, Fitch CA, Stites WE, Garcia-Moreno E B, Biophys J. 2007 Mar 15;92(6):2041-53. Epub 2006 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17172297 17172297]
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[[Category: Micrococcal nuclease]]
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[[Category: Single protein]]
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[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
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[[Category: Garcia-Moreno, E B.]]
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[[Category: Garcia-Moreno EB]]
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[[Category: Gittis, A G.]]
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[[Category: Gittis AG]]
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[[Category: Karp, D A.]]
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[[Category: Karp DA]]
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[[Category: Nuclease]]
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[[Category: Staphylococcal nuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 11:53:29 2008''
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Current revision

Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A

PDB ID 2oxp

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