3oqz: Difference between revisions

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-{{Seed}}
-[[Image:3oqz.jpg|left|200px]]
-<!--
+==Semi-synthetic ribonuclease S: meta-cyano-phenylalanine at position 8==
-The line below this paragraph, containing "STRUCTURE_3oqz", creates the "Structure Box" on the page.
+<StructureSection load='3oqz' size='340' side='right'caption='[[3oqz]], [[Resolution|resolution]] 2.50&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'>[[3oqz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OQZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OQZ 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CF:3-CYANO-L-PHENYLALANINE'>3CF</scene></td></tr>
-{{STRUCTURE_3oqz|  PDB=3oqz  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3oqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqz OCA], [https://pdbe.org/3oqz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oqz RCSB], [https://www.ebi.ac.uk/pdbsum/3oqz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqz ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins.
-===Semi-synthetic ribonuclease S: meta-cyano-phenylalanine at position 8===
+Nitrile Bonds as Infrared Probes of Electrostatics in Ribonuclease S.,Fafarman AT, Boxer SG J Phys Chem B. 2010 Sep 30. PMID:20883003<ref>PMID:20883003</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3oqz" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20883003}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20883003 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20883003}}
+__TOC__
+</StructureSection>
-==About this Structure==
-OQZ is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OQZ OCA].
-==Reference==
-<ref group="xtra">PMID:20883003</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Boxer, S G.]]
+[[Category: Boxer SG]]
-[[Category: Fafarman, A T.]]
+[[Category: Fafarman AT]]
-[[Category: Artificial]]
-[[Category: Cyano]]
-[[Category: Cyanophenylalanine]]
-[[Category: Hydrolase]]
-[[Category: Nitrile]]
-[[Category: Non-natural]]
-[[Category: Probe]]
-[[Category: Vibrational]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 20 06:40:38 2010''