7ppt: Difference between revisions
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==Structure of diFe-Sulerythrin at 0.26 MGy total absorbed dose== | ==Structure of diFe-Sulerythrin at 0.26 MGy total absorbed dose== | ||
<StructureSection load='7ppt' size='340' side='right'caption='[[7ppt]]' scene=''> | <StructureSection load='7ppt' size='340' side='right'caption='[[7ppt]], [[Resolution|resolution]] 1.42Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PPT FirstGlance]. <br> | <table><tr><td colspan='2'>[[7ppt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PPT FirstGlance]. <br> | ||
</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=7ppt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ppt OCA], [https://pdbe.org/7ppt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ppt RCSB], [https://www.ebi.ac.uk/pdbsum/7ppt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ppt ProSAT]</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]] 1.42Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=7ppt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ppt OCA], [https://pdbe.org/7ppt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ppt RCSB], [https://www.ebi.ac.uk/pdbsum/7ppt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ppt ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/F9VPE5_SULTO F9VPE5_SULTO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Protein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron-sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron-sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H2O2. Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis. | |||
Determining the oxidation state of elements by X-ray crystallography.,Lennartz F, Jeoung JH, Ruenger S, Dobbek H, Weiss MS Acta Crystallogr D Struct Biol. 2022 Feb 1;78(Pt 2):238-247. doi:, 10.1107/S2059798321013048. Epub 2022 Jan 24. PMID:35102889<ref>PMID:35102889</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7ppt" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Sulfurisphaera tokodaii str. 7]] | |||
[[Category: Lennartz F]] | [[Category: Lennartz F]] | ||
[[Category: Weiss MS]] | [[Category: Weiss MS]] | ||
Latest revision as of 16:07, 1 February 2024
Structure of diFe-Sulerythrin at 0.26 MGy total absorbed doseStructure of diFe-Sulerythrin at 0.26 MGy total absorbed dose
Structural highlights
FunctionPublication Abstract from PubMedProtein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron-sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron-sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H2O2. Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis. Determining the oxidation state of elements by X-ray crystallography.,Lennartz F, Jeoung JH, Ruenger S, Dobbek H, Weiss MS Acta Crystallogr D Struct Biol. 2022 Feb 1;78(Pt 2):238-247. doi:, 10.1107/S2059798321013048. Epub 2022 Jan 24. PMID:35102889[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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