1air: Difference between revisions

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<StructureSection load='1air' size='340' side='right'caption='[[1air]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1air' size='340' side='right'caption='[[1air]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1air]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AIR FirstGlance]. <br>
<table><tr><td colspan='2'>[[1air]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_chrysanthemi Dickeya chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AIR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1air FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1air OCA], [https://pdbe.org/1air PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1air RCSB], [https://www.ebi.ac.uk/pdbsum/1air PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1air ProSAT]</span></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=1air FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1air OCA], [https://pdbe.org/1air PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1air RCSB], [https://www.ebi.ac.uk/pdbsum/1air PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1air ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH]] Involved in maceration and soft-rotting of plant tissue.  
[https://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH] Involved in maceration and soft-rotting of plant tissue.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1air 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=1air ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics techniques to a resolution of 2.2 A and an R factor (an agreement factor between observed structure factor amplitudes) of 16.1%. The final model consists of all 355 amino acids and 157 water molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.721[deg] for bond angles. The structure of PelE bound to a lanthanum ion, which inhibits the enzymatic activity, has also been refined and compared to the metal-free protein. In addition, the structures of pectate lyase C (PelC) in the presence and absence of a lutetium ion have been refined further using an improved algorithm for identifying waters and other solvent molecules. The two putative active site regions of PelE have been compared to those in the refined structure of PelC. The analysis of the atomic details of PelE and PelC in the presence and absence of lanthanide ions provides insight into the enzymatic mechanism of pectate lyases.
The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.,Lietzke SE, Scavetta RD, Yoder MD, Jurnak F Plant Physiol. 1996 May;111(1):73-92. PMID:12226275<ref>PMID:12226275</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1air" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Erwinia chrysanthemi]]
[[Category: Dickeya chrysanthemi]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pectate lyase]]
[[Category: Jurnak FA]]
[[Category: Jurnak, F A]]
[[Category: Lietzke SE]]
[[Category: Lietzke, S E]]
[[Category: Scavetta RD]]
[[Category: Scavetta, R D]]
[[Category: Yoder MD]]
[[Category: Yoder, M D]]
[[Category: Pectate cleavage]]
[[Category: Pectinolyitc activity]]
[[Category: Trans-elimination]]

Revision as of 18:25, 13 March 2024

PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERSPECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS

Structural highlights

1air is a 1 chain structure with sequence from Dickeya chrysanthemi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLYC_DICCH Involved in maceration and soft-rotting of plant tissue.

Evolutionary Conservation

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

1air, resolution 2.20Å

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OCA
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