2d4j

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{{Seed}}
 
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[[Image:2d4j.png|left|200px]]
 
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==Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution==
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The line below this paragraph, containing "STRUCTURE_2d4j", creates the "Structure Box" on the page.
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<StructureSection load='2d4j' size='340' side='right'caption='[[2d4j]], [[Resolution|resolution]] 1.16&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2d4j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4J FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.16&#8491;</td></tr>
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<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=NO3:NITRATE+ION'>NO3</scene></td></tr>
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{{STRUCTURE_2d4j| PDB=2d4j | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4j OCA], [https://pdbe.org/2d4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4j RCSB], [https://www.ebi.ac.uk/pdbsum/2d4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4j ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/2d4j_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2d4j ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Two monoclinic crystals (space group P2(1)) of hen egg-white lysozyme, a type I crystal grown at room temperature in a D2O solution with pD 4.5 containing 2%(w/v) sodium nitrate and a type II crystal grown at 313 K in a 10%(w/v) sodium chloride solution with pH 7.6, were each transformed into another monoclinic crystal with the same space group by dehydration-induced phase transition. Changes in X-ray diffraction were recorded to monitor the progress of the crystal transformation, which started with the appearance of diffuse streaks. In both crystals, the intensity of h + l odd reflections gradually weakened and finally disappeared on completion of the transformation. X-ray diffraction in the intermediate state indicated the presence of lattices of both the native and transformed crystals. In the native type I crystal, two alternate conformations were observed in the main chain of the region Gly71-Asn74. One conformer bound a sodium ion which was replaced with a water molecule in the other conformer. In the transformed crystal, the sodium ion was removed and the main-chain conformation of this region was converted to that of the water-bound form. The transformed crystal diffracted to a higher resolution than the native crystal, while the peak width of the diffraction spots increased. Analysis of the thermal motion of protein molecules using the TLS model has shown that the enhancement of the diffraction power in the transformed crystal is mainly ascribable to the suppression of rigid-body motion owing to an increase in intermolecular contacts as a result of the loss of bulk solvent.
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===Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution===
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Structural phase transition of monoclinic crystals of hen egg-white lysozyme.,Harata K, Akiba T Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):375-82. Epub 2006, Mar 18. PMID:16552138<ref>PMID:16552138</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2d4j" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16552138}}, adds the Publication Abstract to the page
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16552138 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16552138}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2D4J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA].
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==Reference==
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<ref group="xtra">PMID:16552138</ref><references group="xtra"/>
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[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
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[[Category: Lysozyme]]
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[[Category: Large Structures]]
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[[Category: Akiba, T.]]
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[[Category: Akiba T]]
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[[Category: Harata, K.]]
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[[Category: Harata K]]
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[[Category: Phase transition]]
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[[Category: Rigid-body motion]]
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[[Category: Tls analysis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:52:49 2009''
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Current revision

Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution

PDB ID 2d4j

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