3W9V

Crystal structure of refolded DING protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.031 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation.

Gai, Z.Q., Nakamura, A., Tanaka, Y., Hirano, N., Tanaka, I., Yao, M.

(2013) J.SYNCHROTRON RADIAT. 20: 854-858

  • DOI: 10.1107/S0909049513020694
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • 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 ...

    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 Å 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.

    Organizational Affiliation: 

    Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphate-binding protein
A, B
376Unknown prokaryotic organismMutation(s): 1 
Find proteins for P85173 (Unknown prokaryotic organism)
Go to UniProtKB:  P85173
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.031 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.340α = 90.00
b = 86.890β = 90.81
c = 88.640γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description