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152l

From Proteopedia

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(New page: 200px<br /><applet load="152l" size="450" color="white" frame="true" align="right" spinBox="true" caption="152l, resolution 2.0&Aring;" /> '''CONSERVATION OF SOLVE...)
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[[Image:152l.jpg|left|200px]]<br /><applet load="152l" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="152l, resolution 2.0&Aring;" />
 
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'''CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 LYSOZYME'''<br />
 
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==Overview==
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==CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 LYSOZYME==
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Solvent-binding sites were compared in 10 different crystal forms of phage, T4 lysozyme that were refined using data from 2.6 A to 1.7 A resolution., The sample included 18 crystallographically independent lysozyme, molecules. Despite different crystallization conditions, variable crystal, contacts, changes due to mutation, and varying attention to solvent during, crystallographic refinement, 62% of the 20 most frequently occupied sites, were conserved. Allowing for potential steric interference from, neighboring molecules in the crystal lattice, this fraction increased to, 79% of the sites. There was, however, no solvent-binding site that was, occupied in all 18 lysozyme molecules. A buried double site was occupied, in 17 instances and 2 other internal sites were occupied 15 times. Apart, from these buried sites, the most frequently occupied sites were often at, the amino-termini of alpha-helices. Solvent molecules at the most, conserved sites tended to have crystallographic thermal factors lower than, average, but atoms with low B-factors were not restricted to these sites., Although superficial inspection may suggest that only 50-60% (or less) of, solvent-binding sites are conserved in different crystal forms of a, protein, it appears that many sites appear to be empty either because of, steric interference or because the apparent occupancy of a given site can, vary from crystal to crystal. The X-ray method of identifying sites is, somewhat subjective and tends to result in specification only of those, solvent molecules that are well ordered and bound with high occupancy, even though there is clear evidence for solvent bound at many additional, sites.(ABSTRACT TRUNCATED AT 250 WORDS)
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<StructureSection load='152l' size='340' side='right'caption='[[152l]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[152l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=152L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=152L FirstGlance]. <br>
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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]] 2&#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=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=152l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=152l OCA], [https://pdbe.org/152l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=152l RCSB], [https://www.ebi.ac.uk/pdbsum/152l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=152l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</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/52/152l_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=152l ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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152L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t2 Enterobacteria phage t2] with SO4 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=152L OCA].
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==Reference==
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<references/>
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Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme., Zhang XJ, Matthews BW, Protein Sci. 1994 Jul;3(7):1031-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7920248 7920248]
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__TOC__
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[[Category: Enterobacteria phage t2]]
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</StructureSection>
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[[Category: Lysozyme]]
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[[Category: Escherichia virus T4]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Matsumura, M.]]
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[[Category: Matsumura M]]
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[[Category: Matthews, B.W.]]
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[[Category: Matthews BW]]
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[[Category: Weaver, L.H.]]
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[[Category: Weaver LH]]
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[[Category: SO4]]
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[[Category: hydrolase(o-glycosyl)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:27:52 2007''
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Current revision

CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 LYSOZYME

PDB ID 152l

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