2w1m: Difference between revisions

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-{{Seed}}
-[[Image:2w1m.png|left|200px]]
-<!--
+==THE INTERDEPENDENCE OF WAVELENGTH, REDUNDANCY AND DOSE IN SULFUR SAD EXPERIMENTS: 2.070 A WAVELENGTH with 2theta 30 degrees data==
-The line below this paragraph, containing "STRUCTURE_2w1m", creates the "Structure Box" on the page.
+<StructureSection load='2w1m' size='340' side='right'caption='[[2w1m]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2w1m]] 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=2W1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W1M FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
--->
+<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></td></tr>
-{{STRUCTURE_2w1m|  PDB=2w1m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w1m OCA], [https://pdbe.org/2w1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w1m RCSB], [https://www.ebi.ac.uk/pdbsum/2w1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w1m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+== 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/w1/2w1m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2w1m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the last decade, the popularity of sulfur SAD anomalous dispersion experiments has spread rapidly among synchrotron users as a quick and streamlined way of solving the phase problem in macromolecular crystallography. On beamline 10 at SRS (Daresbury Laboratory, UK), a versatile design has allowed test data sets to be collected at six wavelengths between 0.979 and 2.290 A in order to evaluate the importance and the interdependence of experimental variables such as the Bijvoet ratio, wavelength, resolution limit, data redundancy and absorbed X-ray dose in the sample per data set. All the samples used in the experiments were high-quality hen egg-white lysozyme crystals. X-radiation damage was found to affect disulfide bridges after the crystals had been given a total dose of 0.20 x 10(7) Gy. However, with such a total dose, it was still possible in all cases to find a strategy to collect data sets to determine the sulfur substructure and produce good-quality phases by choosing an optimum combination of wavelength, exposure time and redundancy. A |Delta(ano)|/sigma(Delta(ano)) greater than 1.5 for all resolution shells was a necessary requirement for successful sulfur SAD substructure location. Provided this is achieved, it seems possible to find an optimum compromise between wavelength, redundancy and dose to provide phasing information. The choice of the wavelength should then follow the sample composition and the diffracting properties of the crystal. For strongly diffracting crystals, wavelengths equal or shorter than 1.540 A can be selected to capture the available data (provided the Bijvoet ratio is reasonable), while a longer wavelength, to gain as high a Bijvoet ratio as possible, must be used for more weakly diffracting crystals. These results suggest that an approach to a sulfur SAD experiment based on a complete description of the crystal system and the instrument for data collection is useful.
-===THE INTERDEPENDENCE OF WAVELENGTH, REDUNDANCY AND DOSE IN SULFUR SAD EXPERIMENTS: 2.070 A WAVELENGTH WITH 2THETA 30 DEGREES DATA===
+The interdependence of wavelength, redundancy and dose in sulfur SAD experiments.,Cianci M, Helliwell JR, Suzuki A Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1196-209. Epub, 2008 Nov 18. PMID:19018096<ref>PMID:19018096</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2w1m" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19018096}}, adds the Publication Abstract to the page
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19018096 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19018096}}
+__TOC__
+</StructureSection>
-==About this Structure==
-W1M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W1M OCA].
-==Reference==
-The interdependence of wavelength, redundancy and dose in sulfur SAD experiments., Cianci M, Helliwell JR, Suzuki A, Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1196-209. Epub, 2008 Nov 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19018096 19018096]
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Cianci M]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Helliwell JR]]
-[[Category: Detector- tilt geometry]]
+[[Category: Suzuki A]]
-[[Category: Dose]]
-[[Category: Hydrolase]]
-[[Category: Radiation damage]]
-[[Category: Redundancy]]
-[[Category: Sad]]
-[[Category: Wavelength]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  3 20:29:54 2008''