1b20: Difference between revisions

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-[[Image:1b20.gif|left|200px]]
- {{Structure
+==DELETION OF A BURIED SALT-BRIDGE IN BARNASE==
-|PDB= 1b20 |SIZE=350|CAPTION= <scene name='initialview01'>1b20</scene>, resolution 1.7&Aring;
+<StructureSection load='1b20' size='340' side='right'caption='[[1b20]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1b20]] 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=1B20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B20 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b20 OCA], [https://pdbe.org/1b20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b20 RCSB], [https://www.ebi.ac.uk/pdbsum/1b20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b20 ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b20 OCA], [http://www.ebi.ac.uk/pdbsum/1b20 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b20 RCSB]</span>
+== 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/b2/1b20_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=1b20 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Double-mutant cycles are widely used in the field of protein engineering to measure intermolecular and intramolecular interactions. Ideally, there should be no structural rearrangement of the protein on making the two single mutations and the double mutation within the cycle. However, structural pertubation on mutation does not preclude the use of this method, providing the sum of the changes in the single mutants equals the change in the double mutant. In this way, the energy associated with any structural rearrangement cancels in the double-mutant cycle. Previously, the contribution of a buried salt bridge between Arg69 and Asp93 in barnase to the stability of the folded protein has been determined by double-mutant cycle analysis. In order to determine whether the measured interaction of -14.0 kJ mol(-1) represents the true interaction energy, the crystal structure of each mutant within the double-mutant cycle was solved. Although mutation results in structural shifts, the majority of those in the single mutants are also found in the double mutant; their energetic effects in the double-mutant cycle are therefore cancelled. This study highlights the robust nature of the double-mutant cycle analysis.
-'''DELETION OF A BURIED SALT-BRIDGE IN BARNASE'''
+A structural double-mutant cycle: estimating the strength of a buried salt bridge in barnase.,Vaughan CK, Harryson P, Buckle AM, Fersht AR Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):591-600. Epub 2002, Mar 22. PMID:11914482<ref>PMID:11914482</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1b20" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Double-mutant cycles are widely used in the field of protein engineering to measure intermolecular and intramolecular interactions. Ideally, there should be no structural rearrangement of the protein on making the two single mutations and the double mutation within the cycle. However, structural pertubation on mutation does not preclude the use of this method, providing the sum of the changes in the single mutants equals the change in the double mutant. In this way, the energy associated with any structural rearrangement cancels in the double-mutant cycle. Previously, the contribution of a buried salt bridge between Arg69 and Asp93 in barnase to the stability of the folded protein has been determined by double-mutant cycle analysis. In order to determine whether the measured interaction of -14.0 kJ mol(-1) represents the true interaction energy, the crystal structure of each mutant within the double-mutant cycle was solved. Although mutation results in structural shifts, the majority of those in the single mutants are also found in the double mutant; their energetic effects in the double-mutant cycle are therefore cancelled. This study highlights the robust nature of the double-mutant cycle analysis.
+*[[Barnase 3D structures|Barnase 3D structures]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-==About this Structure==
+== References ==
-B20 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=1B20 OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-A structural double-mutant cycle: estimating the strength of a buried salt bridge in barnase., Vaughan CK, Harryson P, Buckle AM, Fersht AR, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):591-600. Epub 2002, Mar 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11914482 11914482]
 [[Category: Bacillus amyloliquefaciens]]
-[[Category: Ribonuclease T(1)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Buckle AM]]
-[[Category: Buckle, A M.]]
+[[Category: Fersht AR]]
-[[Category: Fersht, A R.]]
+[[Category: Harryson P]]
-[[Category: Harryson, P.]]
+[[Category: Oliveberg M]]
-[[Category: Oliveberg, M.]]
+[[Category: Vaughan CK]]
-[[Category: Vaughan, C K.]]
-[[Category: alpha/beta protein]]
-[[Category: microbial ribonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:51:53 2008''