1sf7: Difference between revisions

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-[[Image:1sf7.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1sf7", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1sf7|  PDB=1sf7  |  SCENE=  }}
-'''BINDING OF TETRA-N-ACETYLCHITOTETRAOSE TO HEW LYSOZYME: A POWDER DIFFRACTION STUDY'''
+==BINDING OF TETRA-N-ACETYLCHITOTETRAOSE TO HEW LYSOZYME: A POWDER DIFFRACTION STUDY==
+<StructureSection load='1sf7' size='340' side='right'caption='[[1sf7]], [[Resolution|resolution]] 3.22&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1sf7]] 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=1SF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SF7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray powder diffraction, [[Resolution|Resolution]] 3.22&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1sf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sf7 OCA], [https://pdbe.org/1sf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sf7 RCSB], [https://www.ebi.ac.uk/pdbsum/1sf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sf7 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/sf/1sf7_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=1sf7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC 3.2.1.17) was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitation preparations in 1.0 M NaCl pH 6.0 buffer. The location of each NAGn was easily found from difference Fourier maps generated from structure factors extracted during preliminary Rietveld refinements. Full NAGn-protein structures were subjected to combined Rietveld and stereochemical restraint refinements (Rwp = 2.28-2.59%; Rp = 1.81-2.04%; RF2 = 3.91-5.80%) and revealed binding modes for NAGn that depended on the length of the NAG oligosaccharide. The NAG2 ligand was found in the BC sites in the cleft of HEWL, NAG3 was found to bind in both the ABC and BCD sites in the ratio 35:65 and NAG4 and NAG5 bound to the ABCD and ABCDE sites, respectively, while NAG6 only bound to sites ABCDE, leaving the F site empty with the remaining saccharide ring located in a solvent region adjacent to the A site. All protein powder diffraction patterns in this study consisted of extremely sharp Bragg peaks consistent with approximately 1 microm crystallites that were devoid of line-broadening defects. Details of the stereochemical restraints used in these refinements and their impact on structural validation are also discussed.
-==Overview==
+Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study.,Von Dreele RB Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):22-32. Epub 2004, Dec 17. PMID:15608372<ref>PMID:15608372</ref>
-The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC 3.2.1.17) was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitation preparations in 1.0 M NaCl pH 6.0 buffer. The location of each NAGn was easily found from difference Fourier maps generated from structure factors extracted during preliminary Rietveld refinements. Full NAGn-protein structures were subjected to combined Rietveld and stereochemical restraint refinements (Rwp = 2.28-2.59%; Rp = 1.81-2.04%; RF2 = 3.91-5.80%) and revealed binding modes for NAGn that depended on the length of the NAG oligosaccharide. The NAG2 ligand was found in the BC sites in the cleft of HEWL, NAG3 was found to bind in both the ABC and BCD sites in the ratio 35:65 and NAG4 and NAG5 bound to the ABCD and ABCDE sites, respectively, while NAG6 only bound to sites ABCDE, leaving the F site empty with the remaining saccharide ring located in a solvent region adjacent to the A site. All protein powder diffraction patterns in this study consisted of extremely sharp Bragg peaks consistent with approximately 1 microm crystallites that were devoid of line-broadening defects. Details of the stereochemical restraints used in these refinements and their impact on structural validation are also discussed.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-SF7 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=1SF7 OCA].
+</div>
+<div class="pdbe-citations 1sf7" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study., Von Dreele RB, Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):22-32. Epub 2004, Dec 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15608372 15608372]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Von Dreele RB]]
-[[Category: Dreele, R B.Von.]]
-[[Category: Lysozyme]]
-[[Category: Powder diffraction]]
-[[Category: Rietveld refinement]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:37:43 2008''