5VKF

RHCC in complex with Naphthalene

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Staphylothermus marinus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-04-21 Released: 2018-04-25 
  • Deposition Author(s): McDougall, M., Stetefeld, J.
  • Funding Organization(s): Natural Sciences and Engineering Research Council of Canada- Discovery Grants, Natural Sciences and Engineering Research Council of Canada- Strategic Partnership Grants

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Proteinaceous Nano container Encapsulate Polycyclic Aromatic Hydrocarbons.

McDougall, M.Francisco, O.Harder-Viddal, C.Roshko, R.Heide, F.Sidhu, S.Khajehpour, M.Leslie, J.Palace, V.Tomy, G.T.Stetefeld, J.

(2019) Sci Rep 9: 1058-1058

  • DOI: https://doi.org/10.1038/s41598-018-37323-x
  • Primary Citation of Related Structures:  
    5VH0, 5VKF

  • PubMed Abstract: 

    Polycyclic aromatic hydrocarbons (PAHs) are toxic, mutagenic and among the most damaging chemical compounds with regard to living organisms. Because of their persistence and wide distribution removal from the environment is an important challenge. Here we report a new Nano container matrix based on the deep sea archaea-derived RHCC-Nanotube (RHCC-NT), which rapidly and preferentially binds low molecular weight PAHs. Under controlled-laboratory conditions and using fluorescence spectroscopy in combination with X-ray crystallography and MD simulations, we quantified the real-time binding of low molecular weight PAHs (2-4 rings) to our substrate. Binding coefficients ranged from 5.4 ± 1.6 (fluorene) to 32 ± 7.0 μM (acenaphthylene) and a binding capacity of 85 pmoles PAH per mg RHCC-NT, or 2.12 μmoles in a standard 25 mg sampler. The uptake rate of pyrene was calculated to be 1.59 nmol/hr∙mol RHCC-NT (at 10  C). Our results clearly show that RHCC-NT is uniquely suited as a monitoring matrix for low molecular weight PAHs.


  • Organizational Affiliation

    Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetrabrachion
A, B, C, D
52Staphylothermus marinusMutation(s): 0 
UniProt
Find proteins for Q54436 (Staphylothermus marinus)
Explore Q54436 
Go to UniProtKB:  Q54436
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54436
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.359α = 90
b = 110.359β = 90
c = 70.827γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council of Canada- Discovery GrantsCanadaRGPIN-342077-2012
Natural Sciences and Engineering Research Council of Canada- Strategic Partnership GrantsCanadaSTGP-479210-2015

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description