1bsb: Difference between revisions

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 ==CRYSTAL STRUCTURAL ANALYSIS OF MUTATIONS IN THE HYDROPHOBIC CORES OF BARNASE==
-<StructureSection load='1bsb' size='340' side='right' caption='[[1bsb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1bsb' size='340' side='right'caption='[[1bsb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bsb]] is a 3 chain structure with 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=1BSB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BSB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1bsb]] 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=1BSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BSB FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bsb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bsb RCSB], [http://www.ebi.ac.uk/pdbsum/1bsb PDBsum]</span></td></tr>
+</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&#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=1bsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bsb OCA], [https://pdbe.org/1bsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bsb RCSB], [https://www.ebi.ac.uk/pdbsum/1bsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bsb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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/bs/1bsb_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/1bsb_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1bsb ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-We have solved and analysed the crystal structures of five mutants in the hydrophobic core of barnase to investigate the structural basis for the contribution of hydrophobic residues and side-chain packing to the stability of globular proteins. In case ease, an amino acid side-chain has been replaced with one of smaller volume. The overall structures of four Ile--&gt;Val mutants (residues 51, 76, 88 and 96) and one Leu--&gt;Val mutant (residue 89) are all isomorphous with the wild-type structure. The magnitude and nature of structural shifts in the three hydrophobic core regions of barnase depend on the local environment of the substitution site, but have some features in common. (1) Side-chain atoms move to a greater extent than do main-chain atoms. (2) Repacking at the substitution site is achieved by either a rigid body shift of side-chain atoms (for Ile--&gt;Val76 and Ile--&gt;Val96 mutants), or by a combination of a side-chain shift and rotation (for Ile--&gt;Val51 and Ile--&gt;Val88 mutants). The mutated residue moves to the greatest extent, and generally in the direction of the created cavity (the largest atomic shift is 0.9 A, for Ile--&gt;Val51). The space left behind from such shifts is not seen to be filled by neighbouring side-chains. (3) Where a cavity remains after mutation, it does not contain any solvent molecules. (4) There is no correlation between the extent of structural movements and the atomic temperature factors of atoms that have moved. (5) Structural movements are not large enough to disrupt hydrogen bonding. Valine 88, in the Ile--&gt;Val88 mutant, is disordered and the electron density suggests several side-chain conformations. The reduction in the volumes of the cavities introduced upon mutation, due to collapse of the surrounding structure, ranges from 11% (Ile--&gt;Val96) to 90% (Ile--&gt;Val51).
-Crystal structural analysis of mutations in the hydrophobic cores of barnase.,Buckle AM, Henrick K, Fersht AR J Mol Biol. 1993 Dec 5;234(3):847-60. PMID:8254677<ref>PMID:8254677</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Barnase|Barnase]]
+*[[Barnase 3D structures|Barnase 3D structures]]
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-*[[Temp|Temp]]
-*[[User:Jaime.Prilusky/Test/tree|User:Jaime.Prilusky/Test/tree]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Bacillus amyloliquefaciens]]
-[[Category: Buckle, A M]]
+[[Category: Large Structures]]
-[[Category: Fersht, A R]]
+[[Category: Buckle AM]]
-[[Category: Henrick, K]]
+[[Category: Fersht AR]]
-[[Category: Endonuclease]]
+[[Category: Henrick K]]