2f5w: Difference between revisions

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-[[Image:2f5w.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2f5w", 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),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2f5w|  PDB=2f5w  |  SCENE=  }}
-'''Cross-linked barnase soaked in 3 M thiourea'''
+==Cross-linked barnase soaked in 3 M thiourea==
+<StructureSection load='2f5w' size='340' side='right'caption='[[2f5w]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2f5w]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5W 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]] 2.001&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TOU:THIOUREA'>TOU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2f5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5w OCA], [https://pdbe.org/2f5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5w RCSB], [https://www.ebi.ac.uk/pdbsum/2f5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNBR_BACAM RNBR_BACAM] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.
+== 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/f5/2f5w_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=2f5w ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structural data about the early step of protein denaturation were obtained from cross-linked crystals for two small proteins: barnase and lysozyme. Several denaturant agents like urea, bromoethanol or thiourea were used at increasing concentrations up to a limit leading to crystal disruption (&gt;or=2 to 6 M). Before the complete destruction of the crystal order started, specific binding sites were observed at the protein surfaces, an indication that the preliminary step of denaturation is the disproportion of intermolecular polar bonds to the benefit of the agent "parasiting" the surface. The analysis of the thermal factors first agree with a stabilization effect at low or moderate concentration of denaturants rapidly followed by a destabilization at specific weak points when the number of sites increase (overflooding effect).
-==Overview==
+On the edge of the denaturation process: application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations.,Salem M, Mauguen Y, Prange T Biochim Biophys Acta. 2006 May;1764(5):903-12. Epub 2006 Mar 20. PMID:16600702<ref>PMID:16600702</ref>
-Structural data about the early step of protein denaturation were obtained from cross-linked crystals for two small proteins: barnase and lysozyme. Several denaturant agents like urea, bromoethanol or thiourea were used at increasing concentrations up to a limit leading to crystal disruption (&gt;or=2 to 6 M). Before the complete destruction of the crystal order started, specific binding sites were observed at the protein surfaces, an indication that the preliminary step of denaturation is the disproportion of intermolecular polar bonds to the benefit of the agent "parasiting" the surface. The analysis of the thermal factors first agree with a stabilization effect at low or moderate concentration of denaturants rapidly followed by a destabilization at specific weak points when the number of sites increase (overflooding effect).
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-F5W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5W OCA].
+</div>
+<div class="pdbe-citations 2f5w" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-On the edge of the denaturation process: application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations., Salem M, Mauguen Y, Prange T, Biochim Biophys Acta. 2006 May;1764(5):903-12. Epub 2006 Mar 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16600702 16600702]
+*[[Barnase 3D structures|Barnase 3D structures]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus amyloliquefaciens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Prange, T.]]
+[[Category: Prange T]]
-[[Category: Salem, M.]]
+[[Category: Salem M]]
-[[Category: Barnase]]
-[[Category: Bromoethanol]]
-[[Category: Cross-linked crystal]]
-[[Category: Denaturation]]
-[[Category: Glutaraldehyde]]
-[[Category: Lysozyme]]
-[[Category: Thiourea]]
-[[Category: Urea]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 03:29:47 2008''