1l2k: Difference between revisions

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 ==Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.==
-<StructureSection load='1l2k' size='340' side='right' caption='[[1l2k]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L2K FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l2k OCA], [http://pdbe.org/1l2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l2k RCSB], [http://www.ebi.ac.uk/pdbsum/1l2k PDBsum]</span></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 ==
-[[http://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] 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.
 == 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>
+     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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:12062378<ref>PMID:12062378</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1l2k" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Myoglobin|Myoglobin]]
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Physeter catodon]]
-[[Category: Engler, N]]
+[[Category: Engler N]]
-[[Category: Niimura, N]]
+[[Category: Niimura N]]
-[[Category: Ostermann, A]]
+[[Category: Ostermann A]]
-[[Category: Parak, F G]]
+[[Category: Parak FG]]
-[[Category: Tanaka, I]]
+[[Category: Tanaka I]]
-[[Category: Heme protein]]
-[[Category: Hydration structure]]
-[[Category: Hydrogen atom]]
-[[Category: Neutron structure]]
-[[Category: Oxygen storage-transport complex]]