4OI6

Crystal structure analysis of nickel-bound form SCO4226 from Streptomyces coelicolor A3(2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Streptomyces coelicolor SCO4226 Is a Nickel Binding Protein.

Lu, M.Jiang, Y.L.Wang, S.Jin, H.Zhang, R.G.Virolle, M.J.Chen, Y.Zhou, C.Z.

(2014) PLoS One 9: e109660-e109660

  • DOI: https://doi.org/10.1371/journal.pone.0109660
  • Primary Citation of Related Structures:  
    4OI3, 4OI6

  • PubMed Abstract: 

    The open reading frame SCO4226 of Streptomyces coelicolor A3(2) encodes an 82-residue hypothetical protein. Biochemical assays revealed that each SCO4226 dimer binds four nickel ions. To decipher the molecular function, we solved the crystal structures of SCO4226 in both apo- and nickel-bound (Ni-SCO4226) forms at 1.30 and 2.04 Å resolution, respectively. Each subunit of SCO4226 dimer adopts a canonical ferredoxin-like fold with five β-strands flanked by two α-helices. In the structure of Ni-SCO4226, four nickel ions are coordinated at the surface of the dimer. Further biochemical assays suggested that the binding of Ni2+ triggers the self-aggregation of SCO4226 in vitro. In addition, RT-qPCR assays demonstrated that the expression of SCO4226 gene in S. coelicolor is specifically up-regulated by the addition of Ni2+, but not other divalent ions such as Cu2+, Mn2+ or Co2+. All these results suggested that SCO4226 acts as a nickel binding protein, probably required for nickel sequestration and/or detoxification.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China; Department of Biology, South University of Sciences and Technology of China, Shenzhen, Guangdong, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nickel responsive protein
A, B
89Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO4226
UniProt
Find proteins for Q9FCE4 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9FCE4 
Go to UniProtKB:  Q9FCE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FCE4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.33α = 90
b = 67.14β = 94.98
c = 35.09γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary