4lzt: Difference between revisions

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[[Image:4lzt.jpg|left|200px]]<br /><applet load="4lzt" size="350" color="white" frame="true" align="right" spinBox="true"
caption="4lzt, resolution 0.95&Aring;" />
'''ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K'''<br />


==Overview==
==ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K==
<StructureSection load='4lzt' size='340' side='right'caption='[[4lzt]], [[Resolution|resolution]] 0.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4lzt]] 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=4LZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LZT FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=4lzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lzt OCA], [https://pdbe.org/4lzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lzt RCSB], [https://www.ebi.ac.uk/pdbsum/4lzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lzt ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== 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/lz/4lzt_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=4lzt ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F &gt; 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.
X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F &gt; 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.


==About this Structure==
Refinement of triclinic hen egg-white lysozyme at atomic resolution.,Walsh MA, Schneider TR, Sieker LC, Dauter Z, Lamzin VS, Wilson KS Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):522-46. PMID:9761848<ref>PMID:9761848</ref>
4LZT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with <scene name='pdbligand=NO3:'>NO3</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LZT OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Refinement of triclinic hen egg-white lysozyme at atomic resolution., Walsh MA, Schneider TR, Sieker LC, Dauter Z, Lamzin VS, Wilson KS, Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):522-46. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9761848 9761848]
</div>
<div class="pdbe-citations 4lzt" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
[[Category: Lysozyme]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Dauter Z]]
[[Category: Dauter, Z.]]
[[Category: Lamzin V]]
[[Category: Lamzin, V.]]
[[Category: Schneider T]]
[[Category: Schneider, T.]]
[[Category: Sieker LC]]
[[Category: Sieker, L C.]]
[[Category: Walsh MA]]
[[Category: Walsh, M A.]]
[[Category: Wilson KS]]
[[Category: Wilson, K S.]]
[[Category: NO3]]
[[Category: glycosidase]]
[[Category: hydrolase]]
[[Category: o-glycosyl]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:13:48 2008''