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3w9v

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Crystal structure of refolded DING protein

Structural highlights

3w9v is a 2 chain structure with sequence from Unidentified prokaryotic organism. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.031Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PHBP_UNKP May be involved in atherosclerosis.

Function

PHBP_UNKP Phosphate-binding protein.^[1]

Publication Abstract from PubMed

After crystallization of a certain protein-RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 A resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly.

Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation.,Gai Z, Nakamura A, Tanaka Y, Hirano N, Tanaka I, Yao M J Synchrotron Radiat. 2013 Nov;20(Pt 6):854-8. doi: 10.1107/S0909049513020694., Epub 2013 Sep 29. PMID:24121327^[2]

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

References

↑ Diemer H, Elias M, Renault F, Rochu D, Contreras-Martel C, Schaeffer C, Van Dorsselaer A, Chabriere E. Tandem use of X-ray crystallography and mass spectrometry to obtain ab initio the complete and exact amino acids sequence of HPBP, a human 38-kDa apolipoprotein. Proteins. 2008 Jun;71(4):1708-20. PMID:18076037 doi:10.1002/prot.21866
↑ Gai Z, Nakamura A, Tanaka Y, Hirano N, Tanaka I, Yao M. Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation. J Synchrotron Radiat. 2013 Nov;20(Pt 6):854-8. doi: 10.1107/S0909049513020694., Epub 2013 Sep 29. PMID:24121327 doi:http://dx.doi.org/10.1107/S0909049513020694

1 Structural highlights
2 Disease
3 Function
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/3w9v"

@@ Line 3: / Line 3: @@
 <StructureSection load='3w9v' size='340' side='right'caption='[[3w9v]], [[Resolution|resolution]] 1.03&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3w9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Unkp Unkp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W9V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3w9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified_prokaryotic_organism Unidentified prokaryotic organism]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W9V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.031&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2v3q|2v3q]], [[3g62|3g62]], [[2q9t|2q9t]], [[3w9w|3w9w]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3w9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w9v OCA], [https://pdbe.org/3w9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w9v RCSB], [https://www.ebi.ac.uk/pdbsum/3w9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w9v ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/PHBP_UNKP PHBP_UNKP]] May be involved in atherosclerosis.
+[https://www.uniprot.org/uniprot/PHBP_UNKP PHBP_UNKP] May be involved in atherosclerosis.
 == Function ==
-[[https://www.uniprot.org/uniprot/PHBP_UNKP PHBP_UNKP]] Phosphate-binding protein.<ref>PMID:18076037</ref>
+[https://www.uniprot.org/uniprot/PHBP_UNKP PHBP_UNKP] Phosphate-binding protein.<ref>PMID:18076037</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 29: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Unkp]]
+[[Category: Unidentified prokaryotic organism]]
-[[Category: Gai, Z Q]]
+[[Category: Gai ZQ]]
-[[Category: Hirano, N]]
+[[Category: Hirano N]]
-[[Category: Nakamura, A]]
+[[Category: Nakamura A]]
-[[Category: Tanaka, I]]
+[[Category: Tanaka I]]
-[[Category: Tanaka, Y]]
+[[Category: Tanaka Y]]
-[[Category: Yao, M]]
+[[Category: Yao M]]
-[[Category: Ding]]
-[[Category: Phosphate]]
-[[Category: Phosphate binding apolipoprotein]]
-[[Category: Refolded]]
-[[Category: Transport protein]]

3w9v

From Proteopedia

Current revision

Crystal structure of refolded DING protein

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

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