5JR5

RHCC in Complex with Elemental Sulfur


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1002/prot.25385
  • Structures With Same Primary Citation

  • 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 ...

    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 Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tetrabrachion
A, B, C, D
52Staphylothermus marinusMutation(s): 0 
Find proteins for Q54436 (Staphylothermus marinus)
Go to UniProtKB:  Q54436
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PS9
Query on PS9

Download CCD File 
A
octathiocane
S8
JLQNHALFVCURHW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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