3SO7 | pdb_00003so7

Organophoshatedegrading enzyme (OpdA)-phosphate complex

• PDB DOI: https://doi.org/10.2210/pdb3SO7/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium tumefaciens
• Mutation(s): No 


• Deposited: 2011-06-30 Released: 2011-12-07 
• Deposition Author(s): Ely, F., Pedroso, M., Gahan, L.R., Ollis, D.L., Guddat, L.W., Schenk, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter.

Ely, F., Pedroso, M.M., Gahan, L.R., Ollis, D.L., Guddat, L.W., Schenk, G.

(2011) J Inorg Biochem 106: 19-22

• PubMed: 22112835 
• DOI: https://doi.org/10.1016/j.jinorgbio.2011.09.015
• Primary Citation Related Structures: 
  3SO7


• PubMed Abstract: 
  

  OpdA is a binuclear metalloenzyme that can hydrolyze organophosphate pesticides and nerve agents. In this study the crystal structure of the complex between OpdA and phosphate has been determined to 2.20 Å resolution. The structure shows the phosphate bound in a tripodal mode to the metal ions whereby two of the oxygen atoms of PO(4) are terminally bound to each metal ion and a third oxygen bridges the two metal ions, thus displacing the μOH in the active site. In silico modelling demonstrates that the phosphate moiety of a reaction product, e.g. diethyl phosphate, may bind in the same orientation, positioning the diethyl groups neatly into the substrate binding pocket close to the metal center. Thus, similar to the binuclear metallohydrolases urease and purple acid phosphatase the tripodal arrangement of PO(4) is interpreted in terms of a role of the μOH as a reaction nucleophile.

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Organizational Affiliation: 
• School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.93 kDa 
• Atom Count: 2,791 
• Modeled Residue Count: 329 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A	329	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: opdA
UniProt
Find proteins for Q93LD7 (Agrobacterium tumefaciens) Explore Q93LD7  Go to UniProtKB:  Q93LD7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.189	α = 90
b = 109.189	β = 90
c = 62.932	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Ely, F., Pedroso, M., Gahan, L.R., Ollis, D.L., Guddat, L.W., Schenk, G.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2018-04-18
  Changes: Data collection
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary