2mhr: Difference between revisions
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==STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION== | ==STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION== | ||
<StructureSection load='2mhr' size='340' side='right' caption='[[2mhr]], [[Resolution|resolution]] 1.30Å' scene=''> | <StructureSection load='2mhr' size='340' side='right'caption='[[2mhr]], [[Resolution|resolution]] 1.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2mhr]] is a 1 chain structure | <table><tr><td colspan='2'>[[2mhr]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1mhr 1mhr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MHR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2mhr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mhr OCA], [https://pdbe.org/2mhr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mhr RCSB], [https://www.ebi.ac.uk/pdbsum/2mhr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mhr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/HEMTM_THEHE HEMTM_THEHE]] Myohemerythrin is an oxygen-binding protein found in the retractor muscles of certain worms. The oxygen-binding site contains two iron atoms. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mh/2mhr_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mh/2mhr_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2mhr ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2mhr" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Hendrickson, W A]] | [[Category: Hendrickson, W A]] | ||
[[Category: Sheriff, S]] | [[Category: Sheriff, S]] | ||
[[Category: Oxygen binding]] | [[Category: Oxygen binding]] | ||
Latest revision as of 23:49, 20 October 2021
STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTIONSTRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION
Structural highlights
Function[HEMTM_THEHE] Myohemerythrin is an oxygen-binding protein found in the retractor muscles of certain worms. The oxygen-binding site contains two iron atoms. 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 PubMedThe molecular model of myohemerythrin, an oxygen-carrying protein from sipunculan worms, has been refined by stereochemically restrained least-squares minimization at 1.7/1.3 A resolution to a conventional R-value of 0.158. The estimated positional standard deviation is better than 0.15 A for most of the 979 protein atoms. The average isotropic displacement parameter, B, for the protein atoms is 23.1 A2. This high average B parameter appears to be due to the overall motion of the molecule, which correlates with the observed anisotropic diffraction. The side-chains of seven residues were modeled in two conformations, i.e. the side-chains were discretely disordered, and B parameters for several lysine and glutamate side-chains indicate that they are poorly localized. Of the residues in myohemerythrin, 66% are helical, with 62% occurring in four long alpha-helices with mean values for the backbone torsion angles of phi = -65 degrees, psi = -42 degrees, and for the hydrogen bonds distances of N ... O, 3.0 A and H ... O, 2.1 A, and angles of N ... O = C, 153 degrees, N-H ... O, 157 degrees, and H ... O = C, 147 degrees. For two-thirds of the alpha-helical residues, the torsional rotation of the C alpha-C beta bond, chi 1, is approximately -60 degrees, and for one-third chi 1 is approximately 180 degrees. Although most turns in myohemerythrin are well-categorized by previous classification, two do not fit in established patterns. Also included in the refined model are three sulfate ions, all partially occupied, and 157 water molecules, 40% of which are modeled fully occupied. Only one water molecule is internal to the protein, the remainder occur on the surface and are observed principally between symmetry-related molecules contributing, along with van der Waals' contacts, most of the interactions between molecules. There are eight intermolecular protein-protein hydrogen bonds, of which only four are between well-located atoms. Structure of myohemerythrin in the azidomet state at 1.7/1.3 A resolution.,Sheriff S, Hendrickson WA, Smith JL J Mol Biol. 1987 Sep 20;197(2):273-96. PMID:3681996[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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