5lym: Difference between revisions

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{{Seed}}
[[Image:5lym.png|left|200px]]


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==STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMENT AT 1.8 ANGSTROM RESOLUTION AND A COMPARISON OF THE VARIABLE REGIONS IN THE POLYMORPHIC FORMS==
The line below this paragraph, containing "STRUCTURE_5lym", creates the "Structure Box" on the page.
<StructureSection load='5lym' size='340' side='right'caption='[[5lym]], [[Resolution|resolution]] 1.80&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'>[[5lym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lym 1lym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LYM 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]] 1.8&#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=NO3:NITRATE+ION'>NO3</scene></td></tr>
{{STRUCTURE_5lym|  PDB=5lym  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5lym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lym OCA], [https://pdbe.org/5lym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lym RCSB], [https://www.ebi.ac.uk/pdbsum/5lym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lym 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/ly/5lym_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=5lym ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Monoclinic crystals of hen egg-white lysozyme (E.C. 3.2.1.17, HEL) grown at low pH in the presence of NaNO(3) belong to space group P2(1) with unit-cell dimensions, a = 28.0, b = 62.5, c = 60.9 A and beta= 90.8 degrees with two molecules in the asymmetric unit. 1.8 A resolution intensity data, collected on a CAD-4 diffractometer, contained 17 524 reflections with F &gt; 3sigma (93% complete). Our earlier preliminary 1.8 A model was refitted and refined using X-PLOR to an R value of 0.189. The deviations in the model from ideal geometry are 0.013 A in bond lengths and 2.8 degrees in bond angles. The r.m.s. deviation in the backbone atoms between the two molecules is 0.42 A. A comparison of HEL in different polymorphic crystal forms reveals that the prominent structural variability among them resides in two exposed regions 45-50 and 65-73 which are also regions of lattice contacts.


===STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMENT AT 1.8 ANGSTROM RESOLUTION AND A COMPARISON OF THE VARIABLE REGIONS IN THE POLYMORPHIC FORMS===
Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms.,Rao ST, Sundaralingam M Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):170-5. PMID:15299739<ref>PMID:15299739</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5lym" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_15299739}}, adds the Publication Abstract to the page
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 15299739 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_15299739}}
__TOC__
 
</StructureSection>
==About this Structure==
5LYM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lym 1lym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LYM OCA].
 
==Reference==
Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms., Rao ST, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):170-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299739 15299739]
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
[[Category: Lysozyme]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Rao ST]]
[[Category: Rao, S T.]]
[[Category: Sundaralingam M]]
[[Category: Sundaralingam, M.]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul  3 14:05:52 2008''

Latest revision as of 08:41, 5 June 2024

STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMENT AT 1.8 ANGSTROM RESOLUTION AND A COMPARISON OF THE VARIABLE REGIONS IN THE POLYMORPHIC FORMSSTUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMENT AT 1.8 ANGSTROM RESOLUTION AND A COMPARISON OF THE VARIABLE REGIONS IN THE POLYMORPHIC FORMS

Structural highlights

5lym is a 2 chain structure with sequence from Gallus gallus. This structure supersedes the now removed PDB entry 1lym. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:
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

Monoclinic crystals of hen egg-white lysozyme (E.C. 3.2.1.17, HEL) grown at low pH in the presence of NaNO(3) belong to space group P2(1) with unit-cell dimensions, a = 28.0, b = 62.5, c = 60.9 A and beta= 90.8 degrees with two molecules in the asymmetric unit. 1.8 A resolution intensity data, collected on a CAD-4 diffractometer, contained 17 524 reflections with F > 3sigma (93% complete). Our earlier preliminary 1.8 A model was refitted and refined using X-PLOR to an R value of 0.189. The deviations in the model from ideal geometry are 0.013 A in bond lengths and 2.8 degrees in bond angles. The r.m.s. deviation in the backbone atoms between the two molecules is 0.42 A. A comparison of HEL in different polymorphic crystal forms reveals that the prominent structural variability among them resides in two exposed regions 45-50 and 65-73 which are also regions of lattice contacts.

Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms.,Rao ST, Sundaralingam M Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):170-5. PMID:15299739[2]

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

See Also

References

  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. ↑ Rao ST, Sundaralingam M. Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms. Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):170-5. PMID:15299739 doi:10.1107/S0907444995009504

5lym, resolution 1.80Å

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