2pw5: Difference between revisions

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==Crystal Structure of Staphylococcal nuclease variant V66Y/P117G/H124L/S128A at room temperature==
The line below this paragraph, containing "STRUCTURE_2pw5", creates the "Structure Box" on the page.
<StructureSection load='2pw5' size='340' side='right'caption='[[2pw5]], [[Resolution|resolution]] 2.10&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'>[[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>
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]] 2.1&#8491;</td></tr>
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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=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>
{{STRUCTURE_2pw5|  PDB=2pw5 |  SCENE= }}
</table>
== Function ==
[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>
    <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=2pw5 ConSurf].
<div style="clear:both"></div>


'''Crystal Structure of Staphylococcal nuclease variant V66Y/P117G/H124L/S128A at room temperature'''
==See Also==
 
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
==About this Structure==
2PW5 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=2PW5 OCA].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/18178652 18178652]
[[Category: Micrococcal nuclease]]
[[Category: Single protein]]
[[Category: Staphylococcus aureus]]
[[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]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:39:49 2008''

Latest revision as of 12:12, 21 February 2024

Crystal Structure of Staphylococcal nuclease variant V66Y/P117G/H124L/S128A at room temperatureCrystal Structure of Staphylococcal nuclease variant V66Y/P117G/H124L/S128A at room temperature

Structural highlights

2pw5 is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A5A520_STAAU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2pw5, resolution 2.10Å

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