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1ljn

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Revision as of 11:12, 12 October 2017

Crystal Structure of Tuekey Egg Lysozyme Complex with Di-N-acetylchitobiose at 1.19A Resolution

Structural highlights

1ljn is a 1 chain structure with sequence from Common turkey. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1lzy
Activity:	Lysozyme, with EC number 3.2.1.17
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LYSC_MELGA] 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.

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

The crystal structure of turkey egg lysozyme (TEL) complexed with di-N-acetylchitobiose (NAG2) was refined at 1.19 A resolution by the full-matrix least-squares method with anisotropic temperature factors, and its thermal motion was evaluated by the TLS method. The average ESDs of atomic parameters of nonhydrogen atoms were 0.030 A for coordinates and 0.025 A(2) for anisotropic temperature factors. The active site cleft of TEL binds the alpha-anomer of NAG2 in a nonproductive binding mode with its pyranose rings parallel to a beta-sheet. The TEL structure was compared with the re-refined 1.12 A structure of native TEL. The RMS difference for equivalent Calpha atoms was 0.103 A and a relatively large difference was observed in the region of residues 104-125 rather than in the beta-sheet region where NAG2 was bound. In contrast, the temperature factor of the beta-sheet region was significantly decreased by the NAG2 binding. The TLS model that describes the rigid body motion in translation, libration, and screw motion was adopted for the evaluation of the molecular motion of TEL and NAG2, and the TLS parameters were determined by the least-squares fit to U(ij). The contribution of the external motion of TEL was estimated to be 55.8% of the observed temperature factor for the native structure and 45.9% for the NAG2 complex. The internal motion of TEL represented with atomic thermal ellipsoids was very similar between the native and complex structures except the NAG2 binding region. In the structure of NAG2, the rigid body motion dominates the thermal motion. The center of rotation of NAG2, 4.45A far from the center of gravity, is on the nitrogen atom of the acetylamino group that is hydrogen bonded to the main-chain peptide groups of Asn49 and Ala107. The rigid body motion of NAG2 indicates that the acetylamino group is most strongly bound to the active site, and the recognition of this group is a crucial step of the substrate binding.

Crystallographic dissection of the thermal motion of protein-sugar complex.,Harata K, Kanai R Proteins. 2002 Jul 1;48(1):53-62. PMID:12012337^[1]

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

References

↑ Harata K, Kanai R. Crystallographic dissection of the thermal motion of protein-sugar complex. Proteins. 2002 Jul 1;48(1):53-62. PMID:12012337 doi:10.1002/prot.10127

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ljn"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Tuekey Egg Lysozyme Complex with Di-N-acetylchitobiose at 1.19A Resolution==
 <StructureSection load='1ljn' size='340' side='right' caption='[[1ljn]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ljn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Meleagris_gallopavo Meleagris gallopavo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ljn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_turkey Common turkey]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LJN FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBS:DI(N-ACETYL-D-GLUCOSAMINE)'>CBS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lzy|1lzy]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ljn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljn OCA], [http://pdbe.org/1ljn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljn RCSB], [http://www.ebi.ac.uk/pdbsum/1ljn PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ljn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljn OCA], [http://pdbe.org/1ljn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ljn RCSB], [http://www.ebi.ac.uk/pdbsum/1ljn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljn ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1ljn ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 36: / Line 37: @@
 __TOC__
 </StructureSection>
+[[Category: Common turkey]]
 [[Category: Lysozyme]]
-[[Category: Meleagris gallopavo]]
 [[Category: Harata, K]]
 [[Category: Kanai, R]]

1ljn

From Proteopedia

Revision as of 11:12, 12 October 2017

Crystal Structure of Tuekey Egg Lysozyme Complex with Di-N-acetylchitobiose at 1.19A Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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