1l2k: Difference between revisions

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New page: left|200px<br /><applet load="1l2k" size="450" color="white" frame="true" align="right" spinBox="true" caption="1l2k, resolution 1.50Å" /> '''Neutron Structure De...
 
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[[Image:1l2k.gif|left|200px]]<br /><applet load="1l2k" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1l2k, resolution 1.50&Aring;" />
'''Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.'''<br />


==Overview==
==Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.==
From the first days of protein neutron structure determination sperm whale, myoglobin was an object under investigation [Nature 224 (1969) 143, J., Mol. Biol. 220 (1991) 381]. Nevertheless myoglobin is still of interest, [Proc. Natl. Acad. Sci. USA 97 (2000) 3872]. The feasibility of the, monochromatic neutron diffractometer BIX-3 at the JRR-3M reactor at the, JAERI [J. Phys. Chem. Solids 60 (1999) 1623], to collect high-resolution, diffraction data in a relatively short time stimulated us to repeat the, structural determination of myoglobin. The structure of metmyoglobin has, been determined up to a resolution of 1.5 A. The hydrogen atoms were, replaced in part, by deuterium soaking the crystals for more than 10 years, in D(2)O. A refinement of all atoms has been performed including the, refinement of individual mean square displacements and occupancies of the, exchangeable protons in backbone hydrogen bonds. A method is described to, show clear negative scattering densities of the H atoms. Water molecules, within the protein and on the molecule surface are shown. The, exchangeability of H atoms is correlated with structural distribution and, flexibility.
<StructureSection load='1l2k' size='340' side='right'caption='[[1l2k]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1l2k]] 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=1L2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L2K FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=ND4:AMMONIUM+CATION+WITH+D'>ND4</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=1l2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l2k OCA], [https://pdbe.org/1l2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l2k RCSB], [https://www.ebi.ac.uk/pdbsum/1l2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l2k ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
== 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/l2/1l2k_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=1l2k ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1L2K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon] with SO4, ND4, HEM and DOD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1L2K OCA].
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution., Ostermann A, Tanaka I, Engler N, Niimura N, Parak FG, Biophys Chem. 2002 Mar 28;95(3):183-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12062378 12062378]
[[Category: Large Structures]]
[[Category: Physeter catodon]]
[[Category: Physeter catodon]]
[[Category: Single protein]]
[[Category: Engler N]]
[[Category: Engler, N.]]
[[Category: Niimura N]]
[[Category: Niimura, N.]]
[[Category: Ostermann A]]
[[Category: Ostermann, A.]]
[[Category: Parak FG]]
[[Category: Parak, F.G.]]
[[Category: Tanaka I]]
[[Category: Tanaka, I.]]
[[Category: DOD]]
[[Category: HEM]]
[[Category: ND4]]
[[Category: SO4]]
[[Category: heme protein]]
[[Category: hydration structure]]
[[Category: hydrogen atoms]]
[[Category: neutron structure]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:11:28 2007''

Latest revision as of 10:29, 14 February 2024

Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.

Structural highlights

1l2k is a 1 chain structure with sequence from Physeter catodon. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Neutron Diffraction, Resolution 1.5Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYG_PHYMC Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1l2k, resolution 1.50Å

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OCA
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