1kf5: Difference between revisions

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-[[Image:1kf5.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1kf5", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1kf5|  PDB=1kf5  |  SCENE=  }}
-'''Atomic Resolution Structure of RNase A at pH 7.1'''
+==Atomic Resolution Structure of RNase A at pH 7.1==
+<StructureSection load='1kf5' size='340' side='right'caption='[[1kf5]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kf5]] is a 1 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=1KF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KF5 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]] 1.15&#8491;</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=1kf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kf5 OCA], [https://pdbe.org/1kf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kf5 RCSB], [https://www.ebi.ac.uk/pdbsum/1kf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kf5 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>
+== 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/kf/1kf5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1kf5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.
-==Overview==
+Atomic resolution structures of ribonuclease A at six pH values.,Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):441-50. Epub 2002, Feb 21. PMID:11856829<ref>PMID:11856829</ref>
-The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-KF5 is a [[Single protein]] structure of sequence 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=1KF5 OCA].
+</div>
+<div class="pdbe-citations 1kf5" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Atomic resolution structures of ribonuclease A at six pH values., Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L, Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):441-50. Epub 2002, Feb 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11856829 11856829]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Berisio R]]
-[[Category: Berisio, R.]]
+[[Category: Lamzin VS]]
-[[Category: Lamzin, V S.]]
+[[Category: Mazzarella L]]
-[[Category: Mazzarella, L.]]
+[[Category: Sica F]]
-[[Category: Sica, F.]]
+[[Category: Wilson KS]]
-[[Category: Wilson, K S.]]
+[[Category: Zagari A]]
-[[Category: Zagari, A.]]
-[[Category: Crystal]]
-[[Category: Ph]]
-[[Category: Rnase some]]
-[[Category: Soaking]]
-[[Category: Titration]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:40:09 2008''