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3w9v

From Proteopedia

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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 1: / Line 1: @@
 ==Crystal structure of refolded DING protein==
-<StructureSection load='3w9v' size='340' side='right' caption='[[3w9v]], [[Resolution|resolution]] 1.03&Aring;' scene=''>
+<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 [http://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 [http://oca.weizmann.ac.il/oca-docs/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"><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">[[2v3q|2v3q]], [[3g62|3g62]], [[2q9t|2q9t]], [[3w9w|3w9w]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w9v OCA], [http://pdbe.org/3w9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w9v RCSB], [http://www.ebi.ac.uk/pdbsum/3w9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w9v 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=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 ==
-[[http://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 ==
-[[http://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 21: / Line 21: @@
 </div>
 <div class="pdbe-citations 3w9v" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phosphate-binding protein|Phosphate-binding protein]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Unkp]]
+[[Category: Large Structures]]
-[[Category: Gai, Z Q]]
+[[Category: Unidentified prokaryotic organism]]
-[[Category: Hirano, N]]
+[[Category: Gai ZQ]]
-[[Category: Nakamura, A]]
+[[Category: Hirano N]]
-[[Category: Tanaka, I]]
+[[Category: Nakamura A]]
-[[Category: Tanaka, Y]]
+[[Category: Tanaka I]]
-[[Category: Yao, M]]
+[[Category: Tanaka Y]]
-[[Category: Ding]]
+[[Category: Yao M]]
-[[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

Proteopedia Page Contributors and Editors (what is this?)

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