1swz

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[[Image:1swz.gif|left|200px]]
 
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==Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods==
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The line below this paragraph, containing "STRUCTURE_1swz", creates the "Structure Box" on the page.
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<StructureSection load='1swz' size='340' side='right'caption='[[1swz]], [[Resolution|resolution]] 1.06&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'>[[1swz]] 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=1SWZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SWZ 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]] 1.06&#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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
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{{STRUCTURE_1swz| PDB=1swz | 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=1swz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1swz OCA], [https://pdbe.org/1swz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1swz RCSB], [https://www.ebi.ac.uk/pdbsum/1swz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1swz 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/sw/1swz_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=1swz ConSurf].
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<div style="clear:both"></div>
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'''Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods'''
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==See Also==
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==Overview==
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<references/>
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Proteins with more than 1000 non-H atoms and without heavy-atom prosthetic groups are very difficult to solve by ab initio direct methods. T4 lysozyme is being used to explore these limits. The protein has 1309 non-H atoms, seven S atoms, no disulfide bonds and no heavy-atom prosthetic group. It is recalcitrant to structure determination by direct methods using X-ray diffraction data to 0.97 A. It is shown here that it is possible to obtain a truly ab initio structure determination of a variant of the protein that has an Rb+ (Z = 37) binding site. Using diffraction data to 1.06 A resolution, the direct-methods programs SIR2002 and ACORN independently solved the structure in about 20 h. The bound Rb+, which contributes about 1.7% of the total scattering, does not appear to distort the structure or to inhibit refinement (R factor 12.1%). The phases obtained via SIR2002 or ACORN are in good agreement with those from a reference structure obtained from conventional molecular-substitution and refinement procedures (average error in the figure-of-merit-weighted phases of less than 25 degrees). Thus, proteins with more than 1000 atoms that include halide-binding or other such sites may be amenable to structure determination by ab initio direct methods. The direct-methods approaches are also compared with structure determination via use of the anomalous scattering of the Rb+ ion. As shown by examples, high-resolution structures determined by direct methods can be useful in highlighting regions of strain in the protein, including short hydrogen bonds and non-planar peptide groups.
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia virus T4]]
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1SWZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWZ OCA].
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[[Category: Large Structures]]
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[[Category: Matthews BW]]
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==Reference==
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[[Category: Mooers BHM]]
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Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods., Mooers BH, Matthews BW, Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1726-37. Epub 2004, Sep 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15388918 15388918]
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[[Category: Enterobacteria phage t4]]
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[[Category: Lysozyme]]
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[[Category: Single protein]]
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[[Category: Matthews, B W.]]
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[[Category: Mooers, B H.M.]]
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[[Category: Ab initio direct method]]
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[[Category: Rb+ binding site]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:14:04 2008''
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Current revision

Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods

PDB ID 1swz

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