1dpw: Difference between revisions

Latest revision as of 23:54, 20 November 2024

STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH MPD

Structural highlights

1dpw is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.64Å
Ligands:	CL, MRD, TRS
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Hen egg-white lysozyme has been crystallized at slightly alkaline pH using 2-methyl-2,4-pentanediol (MPD) as the precipitant. The crystals are nearly isomorphous to crystals grown at acidic pH using sodium chloride as the precipitant. However, the growth kinetics differ markedly between the two conditions. The major reason for this is a molecule of MPD that binds tightly in between two lysozyme molecules and favors the growth of the crystals along the crystallographic c direction over growth perpendicular to it.

Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD.,Weiss MS, Palm GJ, Hilgenfeld R Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):952-8. PMID:10944331^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021
↑ Weiss MS, Palm GJ, Hilgenfeld R. Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD. Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):952-8. PMID:10944331

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021

[2] Weiss MS, Palm GJ, Hilgenfeld R. Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD. Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):952-8. PMID:10944331

[1]

[2]

@@ Line 1: / Line 1: @@
-[[Image:1dpw.png|left|200px]]
-{{STRUCTURE_1dpw|  PDB=1dpw  |  SCENE=  }}
+==STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH MPD==
+<StructureSection load='1dpw' size='340' side='right'caption='[[1dpw]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dpw]] 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=1DPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DPW FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.64&#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=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1dpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dpw OCA], [https://pdbe.org/1dpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dpw RCSB], [https://www.ebi.ac.uk/pdbsum/1dpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dpw 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/dp/1dpw_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=1dpw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hen egg-white lysozyme has been crystallized at slightly alkaline pH using 2-methyl-2,4-pentanediol (MPD) as the precipitant. The crystals are nearly isomorphous to crystals grown at acidic pH using sodium chloride as the precipitant. However, the growth kinetics differ markedly between the two conditions. The major reason for this is a molecule of MPD that binds tightly in between two lysozyme molecules and favors the growth of the crystals along the crystallographic c direction over growth perpendicular to it.
-===STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH MPD===
+Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD.,Weiss MS, Palm GJ, Hilgenfeld R Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):952-8. PMID:10944331<ref>PMID:10944331</ref>
-{{ABSTRACT_PUBMED_10944331}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1dpw" style="background-color:#fffaf0;"></div>
-[[1dpw]] is a 1 chain structure of [[Hen Egg-White (HEW) Lysozyme]] with 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=1DPW OCA].
 ==See Also==
-*[[Hen Egg-White (HEW) Lysozyme|Hen Egg-White (HEW) Lysozyme]]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010944331</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Hilgenfeld, R.]]
+[[Category: Hilgenfeld R]]
-[[Category: Palm, G J.]]
+[[Category: Palm GJ]]
-[[Category: Weiss, M S.]]
+[[Category: Weiss MS]]
-[[Category: Hydrolase]]
-[[Category: Protein-mpd complex]]

1dpw: Difference between revisions

Latest revision as of 23:54, 20 November 2024

STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH MPD

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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