2anx: Difference between revisions

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New page: left|200px<br /><applet load="2anx" size="450" color="white" frame="true" align="right" spinBox="true" caption="2anx, resolution 1.04Å" /> '''crystal structure of...
 
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[[Image:2anx.gif|left|200px]]<br /><applet load="2anx" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2anx, resolution 1.04&Aring;" />
'''crystal structure of bacteriophage P22 lysozyme mutant L87M'''<br />


==Overview==
==crystal structure of bacteriophage P22 lysozyme mutant L87M==
The X-ray crystal structure of the previously unknown bacteriophage P22, lysozyme, the product of gene 19, has been determined ab initio by direct, methods using the program SIR2002. The presence of several partially, occupied iodine anions and samarium cations augmented the ability of, direct methods to locate all 2268 non-H protein atoms in the asymmetric, unit, making this one of the largest structures to date to be determined, ab initio. The iodides were introduced from a quick soak, which the, crystal survived sufficiently well to diffract to 1.04 angstroms, resolution. The complete heavy-atom substructure contributed 6.6% of the, total scattering power. The initial determination of the structure assumed, that there were two iodide ions in the asymmetric unit, although it was, later determined that these sites correspond to partially occupied, samarium ions. Tests suggested that it is better to overestimate rather, than underestimate the heavy-atom content. While experimental phases from, all of the successful tests were of high quality, the best results came, from a SAD experiment using the programs SHELXD and SHELXE. Nonetheless, ab initio structure determination by direct methods was found to be a, viable alternative to traditional protein crystallographic methods, provided that the X-ray data extend to atomic resolution and heavy atoms, with sufficient scattering power are present in the crystal.
<StructureSection load='2anx' size='340' side='right'caption='[[2anx]], [[Resolution|resolution]] 1.04&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2anx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_virus_P22 Salmonella virus P22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ANX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ANX 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]] 1.04&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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=2anx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2anx OCA], [https://pdbe.org/2anx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2anx RCSB], [https://www.ebi.ac.uk/pdbsum/2anx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2anx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ENLYS_BPP22 ENLYS_BPP22] 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 (By similarity).
== 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/an/2anx_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=2anx ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2ANX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_phage_py54 Yersinia phage py54] with SO4, SM, IOD and MG as [http://en.wikipedia.org/wiki/ligands ligands]. 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=2ANX OCA].
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Extension to 2268 atoms of direct methods in the ab initio determination of the unknown structure of bacteriophage P22 lysozyme., Mooers BH, Matthews BW, Acta Crystallogr D Biol Crystallogr. 2006 Feb;62(Pt 2):165-76. Epub 2006, Jan 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16421448 16421448]
[[Category: Large Structures]]
[[Category: Lysozyme]]
[[Category: Salmonella virus P22]]
[[Category: Single protein]]
[[Category: Matthews BW]]
[[Category: Yersinia phage py54]]
[[Category: Mooers BH]]
[[Category: Matthews, B.W.]]
[[Category: Mooers, B.H.]]
[[Category: IOD]]
[[Category: MG]]
[[Category: SM]]
[[Category: SO4]]
[[Category: atomic resolution]]
[[Category: phage lysozyme]]
[[Category: sm-sad]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:15:12 2007''

Latest revision as of 12:13, 14 February 2024

crystal structure of bacteriophage P22 lysozyme mutant L87Mcrystal structure of bacteriophage P22 lysozyme mutant L87M

Structural highlights

2anx is a 2 chain structure with sequence from Salmonella virus P22. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.04Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENLYS_BPP22 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 (By similarity).

Evolutionary Conservation

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

See Also

2anx, resolution 1.04Å

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