9IQH | pdb_00009iqh

Crystal structure of sulfhydrylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Literature

A one-step route for the conversion of Cd waste into CdS quantum dots by Acidithiobacillus sp. via unique biosynthesis pathways.

Li, X.J.Wang, T.Q.Qi, L.Li, F.W.Xia, Y.Z.Zhang, C.J.Chen, L.X.Lin, J.Q.

(2025) RSC Chem Biol 6: 281-294

  • DOI: https://doi.org/10.1039/d4cb00195h
  • Primary Citation of Related Structures:  
    9IQH

  • PubMed Abstract: 

    Microorganisms serve as biological factories for the synthesis of nanomaterials such as CdS quantum dots. Based on the uniqueness of Acidithiobacillus sp., a one-step route was explored to directly convert cadmium waste into CdS QDs using these bacteria. First, an exhaustive study was conducted to reveal the specific pathways involved in the biosynthesis of CdS QDs. The widely known homologous enzyme, cysteine desulfhydrase, which catalyzes the synthesis of CdS QDs from a cysteine substrate, is also present in Acidithiobacillus sp. and is referred to as the OSH enzyme. The structure of the OSH enzyme was determined through X-ray crystallography. Moreover, we identified two new pathways. One involved the SQR enzyme in Acidithiobacillus sp., which catalyzed the formation of sulfur globules and subsequently catalyzed further reactions with GSH to release H 2 S; subsequently, a CdS QD biosynthesis pathway was successfully constructed. The other pathway involved extracellular polyphosphate, a bacterial metabolic product, which with the addition of GSH and Cd 2+ , resulted in the formation of water-soluble fluorescent CdS QDs in the supernatant. Based on the above-described mechanism, after the bioleaching of Cd 2+ from cadmium waste by Acidithiobacillus sp., CdS QDs were directly obtained from the bacterial culture supernatants. This work provides important insights into cleaner production and cadmium bioremediation with potential industrial applications.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Shandong University Qingdao 266237 China lixiaoju@sdu.edu.cn linxuchen@sdu.edu.cn jianqunlin@sdu.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-succinylhomoserine sulfhydrylase
A, B
404Acidithiobacillus ferrooxidansMutation(s): 0 
Gene Names: metZDN052_15485
EC: 2.5.1
UniProt
Find proteins for B7J4S3 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455))
Explore B7J4S3 
Go to UniProtKB:  B7J4S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7J4S3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.732α = 90
b = 82.799β = 110.32
c = 77.496γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271525

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release