3RBT | pdb_00003rbt

Crystal structure of glutathione S-transferase Omega 3 from the silkworm Bombyx mori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.263 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure-guided activity restoration of the silkworm glutathione transferase Omega GSTO3-3

Chen, B.-Y.Ma, X.-X.Guo, P.-C.Tan, X.Li, W.-F.Yang, J.-P.Zhang, N.-N.Chen, Y.Xia, Q.Zhou, C.-Z.

(2011) J Mol Biology 412: 204-211

  • DOI: https://doi.org/10.1016/j.jmb.2011.07.019
  • Primary Citation Related Structures: 
    3RBT

  • PubMed Abstract: 

    Glutathione transferases (GSTs) are ubiquitous detoxification enzymes that conjugate hydrophobic xenobiotics with reduced glutathione. The silkworm Bombyx mori encodes four isoforms of GST Omega (GSTO), featured with a catalytic cysteine, except that bmGSTO3-3 has an asparagine substitution of this catalytic residue. Here, we determined the 2.20-Å crystal structure of bmGSTO3-3, which shares a typical GST overall structure. However, the extended C-terminal segment that exists in all the four bmGSTOs occupies the G-site of bmGSTO3-3 and makes it unworkable, as shown by the activity assays. Upon mutation of Asn29 to Cys and truncation of the C-terminal segment, the in vitro GST activity of bmGSTO3-3 could be restored. These findings provided structural insights into the activity regulation of GSTOs.


  • Organizational Affiliation
    • School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 117.99 kDa 
  • Atom Count: 8,238 
  • Modeled Residue Count: 932 
  • Deposited Residue Count: 984 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione transferase o1
A, B, C, D
246Bombyx moriMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for Q1HPV9 (Bombyx mori)
Explore Q1HPV9 
Go to UniProtKB:  Q1HPV9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1HPV9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.263 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.537α = 90
b = 139.03β = 90
c = 128.816γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description