1e8j: Difference between revisions

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-{{Seed}}
-[[Image:1e8j.png|left|200px]]
-<!--
+==SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS ZINC RUBREDOXIN, NMR, 20 STRUCTURES==
-The line below this paragraph, containing "STRUCTURE_1e8j", creates the "Structure Box" on the page.
+<StructureSection load='1e8j' size='340' side='right'caption='[[1e8j]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1e8j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E8J FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1e8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e8j OCA], [https://pdbe.org/1e8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e8j RCSB], [https://www.ebi.ac.uk/pdbsum/1e8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e8j ProSAT]</span></td></tr>
-{{STRUCTURE_1e8j|  PDB=1e8j  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RUBR_MEGGA RUBR_MEGGA] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.  Electron acceptor for cytoplasmic lactate dehydrogenase.
+== 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/e8/1e8j_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=1e8j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rubredoxins are small, soluble proteins that display a wide variation in thermostability, despite having a high degree of sequence similarity They also vary in the extent to which they are stabilized by solutes such as diglycerol phosphate. Hence, they provide excellent models for studying the mechanisms of thermostabilization. Nuclear magnetic resonance (NMR) spectroscopy can be used to investigate interactions between molecules, as well as subtle changes in conformation in solution, and also provides a means to measure protein stability. The assignment of the proton NMR spectrum of the zinc rubredoxin from Desulfovibrio gigas is presented, together with its structure in solution. The stabilizing effect of diglycerol phosphate on rubredoxin is demonstrated and assessed by determining selected amide proton exchange rates; diglycerol phosphate at 100 mM concentration caused an additional structural stabilization of 1.2 +/-0.4 kJ/mol. The pattern of effects on the exchange rates is discussed in relation to the protein structure.
-===SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS ZINC RUBREDOXIN, NMR, 20 STRUCTURES===
+NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes.,Lamosa P, Brennan L, Vis H, Turner DL, Santos H Extremophiles. 2001 Oct;5(5):303-11. PMID:11699644<ref>PMID:11699644</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e8j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11699644}}, adds the Publication Abstract to the page
+*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11699644 is the PubMed ID number.
+*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_11699644}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-E8J is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E8J OCA].
+[[Category: Large Structures]]
+[[Category: Megalodesulfovibrio gigas]]
-==Reference==
+[[Category: Brennan L]]
-NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes., Lamosa P, Brennan L, Vis H, Turner DL, Santos H, Extremophiles. 2001 Oct;5(5):303-11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11699644 11699644]
+[[Category: Lamosa P]]
-[[Category: Desulfovibrio gigas]]
+[[Category: Santos H]]
-[[Category: Single protein]]
+[[Category: Turner DL]]
-[[Category: Brennan, L.]]
+[[Category: Vis H]]
-[[Category: Lamosa, P.]]
-[[Category: Santos, H.]]
-[[Category: Turner, D L.]]
-[[Category: Vis, H.]]
-[[Category: Iron-sulfur-protein]]
-[[Category: Thermostability]]
-[[Category: Zinc-substitution]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 00:19:17 2008''