2f56: Difference between revisions
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New page: left|200px<br /><applet load="2f56" size="450" color="white" frame="true" align="right" spinBox="true" caption="2f56, resolution 1.955Å" /> '''Barnase cross-linke... |
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== | ==Barnase cross-linked with glutaraldehyde soaked in 6M urea== | ||
Structural data about the early step of protein denaturation were obtained | <StructureSection load='2f56' size='340' side='right'caption='[[2f56]], [[Resolution|resolution]] 1.96Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2f56]] 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=2F56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F56 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]] 1.955Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URE:UREA'>URE</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=2f56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f56 OCA], [https://pdbe.org/2f56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f56 RCSB], [https://www.ebi.ac.uk/pdbsum/2f56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f56 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/f5/2f56_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=2f56 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 (>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). | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2f56" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Barnase 3D structures|Barnase 3D structures]] | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus amyloliquefaciens]] | [[Category: Bacillus amyloliquefaciens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Prange | [[Category: Prange T]] | ||
[[Category: Salem | [[Category: Salem M]] | ||
Latest revision as of 10:43, 23 August 2023
Barnase cross-linked with glutaraldehyde soaked in 6M ureaBarnase cross-linked with glutaraldehyde soaked in 6M urea
Structural highlights
FunctionRNBR_BACAM Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedStructural 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 (>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). 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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