3BXV | pdb_00003bxv

Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.213 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis

Li, M.Chen, Z.Zhang, P.Pan, X.Jiang, C.An, X.Liu, S.Chang, W.

(2008) Biochem Biophys Res Commun 369: 919-923

  • DOI: https://doi.org/10.1016/j.bbrc.2008.02.131
  • Primary Citation Related Structures: 
    3BXV

  • PubMed Abstract: 

    Sulfur oxygenase reductase (SOR) simultaneously catalyzes oxidation and reduction of elemental sulfur to produce sulfite, thiosulfate, and sulfide in the presence of molecular oxygen. In this study, crystal structures of wild type and mutants of SOR from Acidianus tengchongensis (SOR-AT) in two different crystal forms were determined and it was observed that 24 identical SOR monomers form a hollow sphere. Within the icosatetramer sphere, the tetramer and trimer channels were proposed as the paths for the substrate and products, respectively. Moreover, a comparison of SOR-AT with SOR-AA (SOR from Acidianus ambivalens) structures showed that significant differences existed at the active site. Firstly, Cys31 is not persulfurated in SOR-AT structures. Secondly, the iron atom is five-coordinated rather than six-coordinated, since one of the water molecules ligated to the iron atom in the SOR-AA structure is lost. Consequently, the binding sites of substrates and a hypothetical catalytic process of SOR were proposed.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, PR China.

Macromolecule Content 

  • Total Structure Weight: 35.24 kDa 
  • Atom Count: 2,529 
  • Modeled Residue Count: 308 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulfur oxygenase/reductase308N/AMutation(s): 2 
EC: 1.13.11.55
UniProt
Find proteins for Q977W3 (Acidianus tengchongensis)
Explore Q977W3 
Go to UniProtKB:  Q977W3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ977W3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE

Query on FE



Download:Ideal Coordinates CCD File
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.213 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.13α = 90
b = 159.13β = 90
c = 159.13γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2025-04-30
    Changes: Structure summary