5xl0: Difference between revisions

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<StructureSection load='5xl0' size='340' side='right'caption='[[5xl0]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
<StructureSection load='5xl0' size='340' side='right'caption='[[5xl0]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5xl0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XL0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XL0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5xl0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XL0 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=89R:fluorinated+heme'>89R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 1.25&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xl0 OCA], [http://pdbe.org/5xl0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xl0 RCSB], [http://www.ebi.ac.uk/pdbsum/5xl0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xl0 ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=89R:fluorinated+heme'>89R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5xl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xl0 OCA], [https://pdbe.org/5xl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xl0 RCSB], [https://www.ebi.ac.uk/pdbsum/5xl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xl0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.  
[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The orientation of a CF3-substituted heme in sperm whale myoglobin and L29F, H64L, L29F/H64Q, and H64Q variant proteins has been investigated using 19F NMR spectroscopy to elucidate structural factors responsible for the thermodynamic stability of the heme orientational disorder, i.e., the presence of two heme orientations differing by a 180 degrees rotation about the 5-15 meso axis, with respect to the protein moiety. Crystal structure of the met-aquo form of the wild-type myoglobin reconstituted with 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-trifluoromethylporp hyrinatoiron(III), determined at resolution of 1.25 A, revealed the presence of the heme orientational disorder. Alterations of the salt bridge between the heme 13-propionate and Arg45(CD3) side chains due to the mutations resulted in equilibrium constants of the heme orientational disorder ranging between 0.42 and 1.4. Thus, the heme orientational disorder is affected by the salt bridge associated with the heme 13-propionate side chain, confirming the importance of the salt bridge in the heme binding to the protein.
 
Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor.,Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y Biochemistry. 2017 Aug 16. doi: 10.1021/acs.biochem.7b00457. PMID:28758387<ref>PMID:28758387</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xl0" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Physeter catodon]]
[[Category: Physeter catodon]]
[[Category: Harada, A]]
[[Category: Harada A]]
[[Category: Kanai, Y]]
[[Category: Kanai Y]]
[[Category: Nakamura, S]]
[[Category: Nakamura S]]
[[Category: Namiki, K]]
[[Category: Namiki K]]
[[Category: Neya, S]]
[[Category: Neya S]]
[[Category: Nishimura, R]]
[[Category: Nishimura R]]
[[Category: Senda, T]]
[[Category: Senda T]]
[[Category: Shibata, T]]
[[Category: Shibata T]]
[[Category: Suzuki, A]]
[[Category: Suzuki A]]
[[Category: Watanabe, M]]
[[Category: Watanabe M]]
[[Category: Yamamoto, Y]]
[[Category: Yamamoto Y]]
[[Category: Yumoto, F]]
[[Category: Yumoto F]]
[[Category: Fluorinated heme]]
[[Category: Heme orientational disorder]]
[[Category: Myoglobin]]
[[Category: Oxygen transport]]
[[Category: Sperm whale]]
[[Category: Trifluoromethyl group]]

Revision as of 10:19, 27 March 2024

met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a heme possesseing CF3 group as side chain

5xl0, resolution 1.25Å

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