2a7d

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(New page: 200px<br /><applet load="2a7d" size="450" color="white" frame="true" align="right" spinBox="true" caption="2a7d, resolution 1.66&Aring;" /> '''On the Routine Use o...)
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[[Image:2a7d.gif|left|200px]]<br /><applet load="2a7d" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2a7d, resolution 1.66&Aring;" />
 
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'''On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The Optimal Data Collection Wavelength'''<br />
 
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==Overview==
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==On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The Optimal Data Collection Wavelength==
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Complete and highly redundant data sets were collected at different, wavelengths between 0.80 and 2.65 A for a total of ten different protein, and DNA model systems. The magnitude of the anomalous signal-to-noise, ratio as assessed by the quotient R(anom)/R(r.i.m.) was found to be, influenced by the data-collection wavelength and the nature of the, anomalously scattering substructure. By utilizing simple empirical, correlations, for instance between the estimated deltaF/F and the expected, R(anom) or the data-collection wavelength and the expected R(r.i.m.), the, wavelength at which the highest anomalous signal-to-noise ratio can be, expected could be estimated even before the experiment. Almost independent, of the nature of the anomalously scattering substructure and provided that, no elemental X-ray absorption edge is nearby, this optimal wavelength is, 2.1 A.
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<StructureSection load='2a7d' size='340' side='right'caption='[[2a7d]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2a7d]] 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=2A7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A7D 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]] 1.66&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</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=2a7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a7d OCA], [https://pdbe.org/2a7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a7d RCSB], [https://www.ebi.ac.uk/pdbsum/2a7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a7d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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/a7/2a7d_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=2a7d ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Complete and highly redundant data sets were collected at different wavelengths between 0.80 and 2.65 A for a total of ten different protein and DNA model systems. The magnitude of the anomalous signal-to-noise ratio as assessed by the quotient R(anom)/R(r.i.m.) was found to be influenced by the data-collection wavelength and the nature of the anomalously scattering substructure. By utilizing simple empirical correlations, for instance between the estimated deltaF/F and the expected R(anom) or the data-collection wavelength and the expected R(r.i.m.), the wavelength at which the highest anomalous signal-to-noise ratio can be expected could be estimated even before the experiment. Almost independent of the nature of the anomalously scattering substructure and provided that no elemental X-ray absorption edge is nearby, this optimal wavelength is 2.1 A.
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==About this Structure==
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On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.,Mueller-Dieckmann C, Panjikar S, Tucker PA, Weiss MS Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1263-72. Epub 2005, Aug 16. PMID:16131760<ref>PMID:16131760</ref>
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2A7D 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 CL, NA and XE 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=2A7D OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength., Mueller-Dieckmann C, Panjikar S, Tucker PA, Weiss MS, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1263-72. Epub 2005, Aug 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16131760 16131760]
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</div>
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[[Category: Gallus gallus]]
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<div class="pdbe-citations 2a7d" style="background-color:#fffaf0;"></div>
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[[Category: Lysozyme]]
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[[Category: Single protein]]
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[[Category: Mueller-Dieckmann, C.]]
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[[Category: Panjikar, S.]]
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[[Category: Tucker, P.A.]]
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[[Category: Weiss, M.S.]]
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[[Category: CL]]
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[[Category: NA]]
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[[Category: XE]]
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[[Category: hydrolase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:57:44 2007''
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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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<references/>
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__TOC__
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</StructureSection>
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[[Category: Gallus gallus]]
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[[Category: Large Structures]]
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[[Category: Mueller-Dieckmann C]]
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[[Category: Panjikar S]]
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[[Category: Tucker PA]]
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[[Category: Weiss MS]]

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On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The Optimal Data Collection Wavelength

PDB ID 2a7d

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