1kf4: Difference between revisions

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-[[Image:1kf4.png|left|200px]]
-{{STRUCTURE_1kf4|  PDB=1kf4  |  SCENE=  }}
+==Atomic Resolution Structure of RNase A at pH 6.3==
+<StructureSection load='1kf4' size='340' side='right'caption='[[1kf4]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kf4]] 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=1KF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KF4 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]] 1.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1kf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kf4 OCA], [https://pdbe.org/1kf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kf4 RCSB], [https://www.ebi.ac.uk/pdbsum/1kf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kf4 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/1kf4_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=1kf4 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.
-===Atomic Resolution Structure of RNase A at pH 6.3===
+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>
-{{ABSTRACT_PUBMED_11856829}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1kf4" style="background-color:#fffaf0;"></div>
-[[1kf4]] is a 1 chain structure of [[Ribonuclease]] with 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=1KF4 OCA].
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:011856829</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Berisio, R.]]
+[[Category: Berisio R]]
-[[Category: Lamzin, V S.]]
+[[Category: Lamzin VS]]
-[[Category: Mazzarella, L.]]
+[[Category: Mazzarella L]]
-[[Category: Sica, F.]]
+[[Category: Sica F]]
-[[Category: Wilson, K S.]]
+[[Category: Wilson KS]]
-[[Category: Zagari, A.]]
+[[Category: Zagari A]]
-[[Category: Crystal]]
-[[Category: Hydrolase]]
-[[Category: Ph]]
-[[Category: Rnase some]]
-[[Category: Soaking]]
-[[Category: Titration]]