This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5ynx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structure of house dust mite allergen Der f 21 in PEG400

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ynx"

@@ Line 3: / Line 3: @@
 <StructureSection load='5ynx' size='340' side='right'caption='[[5ynx]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<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>
-</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>
+</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>
-<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>
+<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>
+<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>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/ALL21_DERFA ALL21_DERFA]
-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.
-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>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5ynx" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Dermatophagoides farinae]]
 [[Category: Large Structures]]
-[[Category: Beis, K]]
+[[Category: Beis K]]
-[[Category: Chew, F T]]
+[[Category: Chew FT]]
-[[Category: Ho, K L]]
+[[Category: Ho KL]]
-[[Category: Mathavan, I]]
+[[Category: Mathavan I]]
-[[Category: Ng, C L]]
+[[Category: Ng CL]]
-[[Category: Pang, S L]]
+[[Category: Pang SL]]
-[[Category: Rambo, R]]
+[[Category: Rambo R]]
-[[Category: Say, Y H]]
+[[Category: Say YH]]
-[[Category: Teh, A H]]
+[[Category: Teh AH]]
-[[Category: Waterman, J]]
+[[Category: Waterman J]]
-[[Category: Allergen]]

5ynx

From Proteopedia

Current revision

Structure of house dust mite allergen Der f 21 in PEG400

Structural highlights

Function

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox