5ynx

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Current revision (10:24, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5ynx' size='340' side='right'caption='[[5ynx]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
<StructureSection load='5ynx' size='340' side='right'caption='[[5ynx]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ynx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YNX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ynx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dermatophagoides_farinae Dermatophagoides farinae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YNX FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.49&#8491;</td></tr>
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<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=5ynx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynx OCA], [http://pdbe.org/5ynx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynx RCSB], [http://www.ebi.ac.uk/pdbsum/5ynx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynx ProSAT]</span></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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ynx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynx OCA], [https://pdbe.org/5ynx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ynx RCSB], [https://www.ebi.ac.uk/pdbsum/5ynx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynx ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/ALL21_DERFA ALL21_DERFA]
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Dermatophagoides farinae is one of the major house dust mite (HDM) species that cause allergic diseases. N-terminally His-tagged recombinant Der f 21 (rDer f 21), a group 21 allergen, with the signal peptide truncated was successfully overexpressed in an Escherichia coli expression system. The purified rDer f 21 protein was initially crystallized using the sitting-drop vapour-diffusion method. Well diffracting protein crystals were obtained after optimization of the crystallization conditions using the hanging-drop vapour-diffusion method with a reservoir solution consisting of 0.19 M Tris-HCl pH 8.0, 32% PEG 400 at 293 K. X-ray diffraction data were collected to 1.49 A resolution using an in-house X-ray source. The crystal belonged to the C-centered monoclinic space group C2, with unit-cell parameters a = 123.46, b = 27.71, c = 90.25 A, beta = 125.84 degrees . The calculated Matthews coefficient (VM) of 2.06 A(3) Da(-1) suggests that there are two molecules per asymmetric unit, with a solvent content of 40.3%. Despite sharing high sequence identity with Blo t 5 (45%) and Blo t 21 (41%), both of which were determined to be monomeric in solution, size-exclusion chromatography, static light scattering and self-rotation function analysis indicate that rDer f 21 is likely to be a dimeric protein.
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Cloning, expression, purification, characterization, crystallization and X-ray crystallographic analysis of recombinant Der f 21 (rDer f 21) from Dermatophagoides farinae.,Pang SL, Ho KL, Waterman J, Teh AH, Chew FT, Ng CL Acta Crystallogr F Struct Biol Commun. 2015 Nov;71(Pt 11):1396-400. doi:, 10.1107/S2053230X1501818X. Epub 2015 Oct 23. PMID:26527267<ref>PMID:26527267</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5ynx" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Dermatophagoides farinae]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Beis, K]]
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[[Category: Beis K]]
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[[Category: Chew, F T]]
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[[Category: Chew FT]]
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[[Category: Ho, K L]]
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[[Category: Ho KL]]
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[[Category: Mathavan, I]]
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[[Category: Mathavan I]]
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[[Category: Ng, C L]]
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[[Category: Ng CL]]
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[[Category: Pang, S L]]
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[[Category: Pang SL]]
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[[Category: Rambo, R]]
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[[Category: Rambo R]]
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[[Category: Say, Y H]]
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[[Category: Say YH]]
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[[Category: Teh, A H]]
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[[Category: Teh AH]]
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[[Category: Waterman, J]]
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[[Category: Waterman J]]
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[[Category: Allergen]]
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Current revision

Structure of house dust mite allergen Der f 21 in PEG400

PDB ID 5ynx

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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