3kaq: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3kaq.png|left|200px]]
-{{STRUCTURE_3kaq|  PDB=3kaq  |  SCENE=  }}
+==Flavodoxin from D. desulfuricans (semireduced form)==
+<StructureSection load='3kaq' size='340' side='right'caption='[[3kaq]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3kaq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans_ATCC_27774 Desulfovibrio desulfuricans ATCC 27774]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KAQ 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]] 2.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=3kaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kaq OCA], [https://pdbe.org/3kaq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kaq RCSB], [https://www.ebi.ac.uk/pdbsum/3kaq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kaq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FLAW_DESDA FLAW_DESDA] Low-potential electron donor to a number of redox enzymes.
+== 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/ka/3kaq_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=3kaq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of the flavodoxin from Desulfovibrio desulfuricans ATCC 27774 have been determined and refined for both oxidized and semi-reduced forms to final crystallographic R-factors of 17.9% (0.8-0.205-nm resolution) and 19.4% (0.8-0.215-nm resolution) respectively. Native flavodoxin crystals were grown from ammonium sulfate with cell constants a = b = 9.59 nm, c=3.37nm (oxidized crystals) and they belong to space group P3(2)21. Semireduced crystals showed some changes in cell dimensions: a = b = 9.51 nm, c=3.35 nm. The three-dimensional structures are similar to other known flavodoxins and deviations are found essentially in the isoalloxazine ring environment. Conformational changes are observed between both redox states and a flip of the Gly61-Met62 peptide bond occurs upon one-electron reduction of the FMN group. These changes influence the redox potential of the oxidized/semiquinone couple. Modulation of the redox potentials is known to be related to the association constant of the FMN group to the protein. The flavodoxin from D. desulfuricans now studied has a large span between E2 (oxidized --&gt; semiquinone) and E1 (semiquinone --&gt; hydroquinone) redox potentials, both these values being substantially more positive within known flavodoxins. A comparison of their FMN environment was made in both oxidation states in order to correlate functional and structural differences.
-===Flavodoxin from D. desulfuricans (semireduced form)===
+Crystal structure of flavodoxin from Desulfovibrio desulfuricans ATCC 27774 in two oxidation states.,Romero A, Caldeira J, Legall J, Moura I, Moura JJ, Romao MJ Eur J Biochem. 1996 Jul 1;239(1):190-6. PMID:8706707<ref>PMID:8706707</ref>
-{{ABSTRACT_PUBMED_8706707}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3kaq" style="background-color:#fffaf0;"></div>
-[[3kaq]] is a 1 chain structure of [[Flavodoxin]] with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans_subsp._desulfuricans_str._atcc_27774 Desulfovibrio desulfuricans subsp. desulfuricans str. atcc 27774]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KAQ OCA].
 ==See Also==
-*[[Flavodoxin|Flavodoxin]]
+*[[Flavodoxin 3D structures|Flavodoxin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:008706707</ref><references group="xtra"/>
+__TOC__
-[[Category: Desulfovibrio desulfuricans subsp. desulfuricans str. atcc 27774]]
+</StructureSection>
-[[Category: Caldeira, J.]]
+[[Category: Desulfovibrio desulfuricans ATCC 27774]]
-[[Category: LeGall, J.]]
+[[Category: Large Structures]]
-[[Category: Moura, I.]]
+[[Category: Caldeira J]]
-[[Category: Moura, J J.G.]]
+[[Category: LeGall J]]
-[[Category: Romao, M J.]]
+[[Category: Moura I]]
-[[Category: Romero, A.]]
+[[Category: Moura JJG]]
-[[Category: Electron transport]]
+[[Category: Romao MJ]]
-[[Category: Flavodoxin]]
+[[Category: Romero A]]
-[[Category: Flavoprotein]]
-[[Category: Fmn]]
-[[Category: Sulfate-reducing bacteria]]
-[[Category: Transport]]