1swz

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[[Image:1swz.gif|left|200px]]<br /><applet load="1swz" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1swz, resolution 1.06&Aring;" />
 
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'''Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods'''<br />
 
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==Overview==
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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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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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<StructureSection load='1swz' size='340' side='right'caption='[[1swz]], [[Resolution|resolution]] 1.06&Aring;' scene=''>
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== Structural highlights ==
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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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</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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<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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==About this Structure==
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==See Also==
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1SWZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=RB:'>RB</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=BME:'>BME</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWZ 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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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15388918 15388918]
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__TOC__
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[[Category: Bacteriophage t4]]
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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: Matthews, B W.]]
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[[Category: Matthews BW]]
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[[Category: Mooers, B H.M.]]
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[[Category: Mooers BHM]]
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[[Category: BME]]
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[[Category: CL]]
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[[Category: PO4]]
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[[Category: RB]]
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[[Category: ab initio direct methods]]
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[[Category: rb+ binding site]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:06:12 2008''
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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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