5JR5 | pdb_00005jr5

RHCC in Complex with Elemental Sulfur


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PS9Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Archaea S-layer nanotube from a "black smoker" in complex with cyclo-octasulfur (S8 ) rings.

McDougall, M.Francisco, O.Harder-Viddal, C.Roshko, R.Meier, M.Stetefeld, J.

(2017) Proteins 85: 2209-2216

  • DOI: https://doi.org/10.1002/prot.25385
  • Primary Citation of Related Structures:  
    5JR5

  • PubMed Abstract: 

    Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion. Comparisons with earlier MD studies of the free energy of hydration as a function of water occupancy in the same cavity of archaeal tetrabrachion show that the sulfur ring is energetically favored over water.


  • Organizational Affiliation

    Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.52α = 90
b = 110.52β = 90
c = 71.04γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PS9Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description