4NXL | pdb_00004nxl

Dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4NXL

This is version 1.3 of the entry. See complete history

Literature

Structural insights into the stabilization of active, tetrameric DszC by its C-terminus.

Zhang, L.Duan, X.Zhou, D.Dong, Z.Ji, K.Meng, W.Li, G.Li, X.Yang, H.Ma, T.Rao, Z.

(2014) Proteins 82: 2733-2743

  • DOI: https://doi.org/10.1002/prot.24638
  • Primary Citation Related Structures: 
    4NXL

  • PubMed Abstract: 

    Dibenzothiophene (DBT) is a typical sulfur-containing compound found in fossil fuels. This compound and its derivatives are resistant to the hydrodesulfurization method often used in industry, but they are susceptible to enzymatic desulfurization via the 4S pathway, which is a well-studied biochemical pathway consisting of four enzymes. DBT monooxygenase (DszC) from Rhodococcus erythropolis is involved in the first step of the 4S pathway. We determined the crystal structure of DszC, which reveals that, in contrast to several homologous proteins, the C-terminus (410-417) of DszC participates in the stabilization of the substrate-binding pocket. Analytical ultracentrifugation analysis and enzymatic assays confirmed that the C-terminus is important for the stabilization of the active conformation of the substrate-binding pocket and the tetrameric state. Therefore, the C-terminus of DszC plays a significant role in the catalytic activity of this enzyme.


  • Organizational Affiliation
    • College of Life Sciences, Nankai University, Tianjin, China.

Macromolecule Content 

  • Total Structure Weight: 195.62 kDa 
  • Atom Count: 12,786 
  • Modeled Residue Count: 1,596 
  • Deposited Residue Count: 1,812 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DszC
A, B, C, D
453Rhodococcus erythropolisMutation(s): 0 
Gene Names: dszC
EC: 1.14.14.21
UniProt
Find proteins for Q0ZIH5 (Rhodococcus erythropolis)
Explore Q0ZIH5 
Go to UniProtKB:  Q0ZIH5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ZIH5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.98α = 90
b = 136.18β = 90
c = 174.83γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references