6BRI

RHCC with unreduced and reduced Mercury complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Reductive power of the archaea right-handed coiled coil nanotube (RHCC-NT) and incorporation of mercury clusters inside protein cages.

McDougall, M.McEleney, K.Francisco, O.Trieu, B.Ogbomo, E.K.Tomy, G.Stetefeld, J.

(2018) J Struct Biol 203: 281-287

  • DOI: https://doi.org/10.1016/j.jsb.2018.05.013
  • Primary Citation of Related Structures:  
    6BRI

  • PubMed Abstract: 

    Coiled coils are well described as powerful oligomerization motifs and exhibit a large diversity of functions, including gene regulation, cell division, membrane fusion and drug extrusion. The archaea S-layer originated right-handed coiled coil -RHCC-NT- is characterized by extreme stability and is free of cysteine and histidine moieties. In the current study, we have followed a multidisciplinary approach to investigate the capacity of RHCC-NT to bind a variety of ionic complex metal ions. At the outside of the RHCC-NT, one mercury ion forms an electrostatic interaction with the S-methyl moiety of the single methionine residue present in each coil. We demonstrate that RHCC-NT is reducing and incorporating metallic mercury in the large-sized interior cavities which are lined up along the tetrameric channel.


  • Organizational Affiliation

    Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada; Center for Oil and Gas Research and Development (COGRAD), Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Right Handed Coiled Coil
A, B, C, D
52Staphylothermus marinus F1Mutation(s): 0 
Gene Names: Smar_1008
UniProt
Find proteins for A3DN96 (Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1))
Explore A3DN96 
Go to UniProtKB:  A3DN96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DN96
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HGI
Query on HGI

Download Ideal Coordinates CCD File 
HA [auth D]MERCURY (II) IODIDE
Hg I2
YFDLHELOZYVNJE-UHFFFAOYSA-L
HGN
Query on HGN

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DA [auth D],
I [auth A]
mercuriomercury
Hg2
KYKQHSMYWLWROM-UHFFFAOYSA-N
HG
Query on HG

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E [auth A],
L [auth B],
X [auth D]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
IOD
Query on IOD

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AA [auth D]
BA [auth D]
CA [auth D]
F [auth A]
G [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
Y [auth D],
Z [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4
Query on SO4

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R [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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GA [auth D],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

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EA [auth D]
FA [auth D]
S [auth B]
T [auth B]
U [auth B]
EA [auth D],
FA [auth D],
S [auth B],
T [auth B],
U [auth B],
V [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

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J [auth A],
K [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.823α = 90
b = 108.823β = 90
c = 70.388γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-342077-2012
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-004954-2017
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaSTGP 479210-2015

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.3: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description