4Y2I

Gold ion bound to GolB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


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Literature

Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB

Wei, W.Sun, Y.Zhu, M.Liu, X.Sun, P.Wang, F.Gui, Q.Meng, W.Cao, Y.Zhao, J.

(2015) J Am Chem Soc 137: 15358-15361

  • DOI: https://doi.org/10.1021/jacs.5b09895
  • Primary Citation of Related Structures:  
    4Y2I, 4Y2K, 4Y2M

  • PubMed Abstract: 

    The coordination bond between gold and sulfur (Au-S) has been widely studied and utilized in many fields. However, detailed investigations on the basic nature of this bond are still lacking. A gold-specific binding protein, GolB, was recently identified, providing a unique opportunity for the study of the Au-S bond at the molecular level. We probed the mechanical strength of the gold-sulfur bond in GolB using single-molecule force spectroscopy. We measured the rupture force of the Au-S bond to be 165 pN, much lower than Au-S bonds measured on different gold surfaces (∼1000 pN). We further solved the structures of apo-GolB and Au(I)-GolB complex using X-ray crystallography. These structures showed that the average Au-S bond length in GolB is much longer than the reported average value of Au-S bonds. Our results highlight the dramatic influence of the unique biological environment on the stability and strength of metal coordination bonds in proteins.


  • Organizational Affiliation

    Elias James Corey Institute of Biomedical Research, Wuxi Biortus Biosciences Co., Ltd , Jiangyin, 214437, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative metal-binding transport protein65Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: STMDT2_03511
UniProt
Find proteins for A0A140UHB4 (Salmonella typhimurium)
Explore A0A140UHB4 
Go to UniProtKB:  A0A140UHB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140UHB4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.093α = 90
b = 37.093β = 90
c = 169.911γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Science Foundation of ChinaChina21332005
the MOST of ChinaChina2014AA020512
the National Natural Science Foundation of ChinaChina31200607

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations