4OFN | pdb_00004ofn

Monoclinic NaGST1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.330 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.292 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.294 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GSHClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structure of glutathione S-transferase 1 from the major human hookworm parasite Necator americanus (Na-GST-1) in complex with glutathione.

Asojo, O.A.Ceccarelli, C.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1162-1166

  • DOI: https://doi.org/10.1107/S2053230X1401646X
  • Primary Citation of Related Structures:  
    4OFM, 4OFN, 4OFT

  • PubMed Abstract: 

    Glutathione S-transferase 1 from Necator americanus (Na-GST-1) is a vaccine candidate for hookworm infection that has a high affinity for heme and metal porphyrins. As part of attempts to clarify the mechanism of heme detoxification by hookworm GSTs, co-crystallization and soaking studies of Na-GST-1 with the heme-like molecules protoporphyrin IX disodium salt, hematin and zinc protoporphyrin were undertaken. While these studies did not yield the structure of the complex of Na-GST-1 with any of these molecules, co-crystallization experiments resulted in the first structures of the complex of Na-GST-1 with the substrate glutathione. The structures of the complex of Na-GST-1 with glutathione were solved from pathological crystalline aggregates comprising more than one crystal form. These first structures of the complex of Na-GST-1 with the substrate glutathione were solved by molecular replacement from data collected with a sealed-tube home source using the previously reported apo structure as the search model.


  • Organizational Affiliation

    National School of Tropical Medicine, Baylor College of Medicine, Houston, TX 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase-1
A, B
206Necator americanusMutation(s): 0 
Gene Names: gst-1
EC: 2.5.1.18
UniProt
Find proteins for D3U1A5 (Necator americanus)
Explore D3U1A5 
Go to UniProtKB:  D3U1A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3U1A5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.330 (Depositor), 0.330 (DCC) 
  • R-Value Work:  0.292 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.294 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.554α = 90
b = 45.213β = 112.11
c = 113.763γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
PHASERphasing
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GSHClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2014-12-03 
  • Deposition Author(s): Asojo, O.A.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description