6BRI | pdb_00006bri

RHCC with unreduced and reduced Mercury complexes

• PDB DOI: https://doi.org/10.2210/pdb6BRI/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Staphylothermus marinus F1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-30 Released: 2018-02-07 
• Deposition Author(s): McDougall, M., Trieu, B., Stetefeld, J.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 
  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.282 (Depositor), 0.281 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: experimental

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

• PubMed: 29879486 
• DOI: https://doi.org/10.1016/j.jsb.2018.05.013
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada; Center for Oil and Gas Research and Development (COGRAD), Canada.
Manitoba Institute for Materials Science (MIM), University of Manitoba, Canada.
Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada.
Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada; Center for Oil and Gas Research and Development (COGRAD), Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, Canada; Department of Human Anatomy and Cell Science, University of Manitoba, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 27.66 kDa 
• Atom Count: 1,587 
• Modeled Residue Count: 200 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Right Handed Coiled Coil	A, B, C, D	52	Staphylothermus marinus F1	Mutation(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

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HGI	HA [auth D]	MERCURY (II) IODIDE Hg I2 YFDLHELOZYVNJE-UHFFFAOYSA-L
HGN	DA [auth D], I [auth A]	mercuriomercury Hg2 KYKQHSMYWLWROM-UHFFFAOYSA-N
HG	E [auth A], L [auth B], X [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
IOD	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	R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	GA [auth D], W [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	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	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 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.282 (Depositor), 0.281 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.823	α = 90
b = 108.823	β = 90
c = 70.388	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): McDougall, M., Trieu, B., Stetefeld, J.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-342077-2012
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-004954-2017
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	STGP 479210-2015

Revision History  

• 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