6FS3 | pdb_00006fs3

Phosphotriesterase PTE_A53_1

• PDB DOI: https://doi.org/10.2210/pdb6FS3/pdb

• Classification: HYDROLASE
• Organism(s): Brevundimonas diminuta
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-19 Released: 2019-03-20 
• Deposition Author(s): Dym, O., Aggarwal, N., Albeck, S., Unger, T., Hamer Rogotner, S., Silman, I., Leader, H., Ashani, Y., Goldsmith, M., Greisen, P., Tawfik, D., Sussman, L.J.
• Funding Organization(s): DTRA

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of Bacterail Phosphotriesterase variant with high catalytic activity towards organophosphate nerve agents developed by use of structure-based design and molecular evolution

Dym, O., Aggarwal, N., Sussman, J.L., Silman, I.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 73.93 kDa 
• Atom Count: 5,518 
• Modeled Residue Count: 658 
• Deposited Residue Count: 678 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathion hydrolase	A, B	339	Brevundimonas diminuta	Mutation(s): 0  Gene Names: opd EC: 3.1.8.1
UniProt
Find proteins for P0A434 (Brevundimonas diminuta) Explore P0A434  Go to UniProtKB:  P0A434

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9ON	F [auth A], J [auth B]	(2~{S})-2-methylpentanedioic acid C6 H10 O4 AQYCMVICBNBXNA-BYPYZUCNSA-N
ZN	D [auth A], E [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	C [auth A], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.469	α = 90
b = 81.46	β = 95.12
c = 70.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Dym, O., Aggarwal, N., Albeck, S., Unger, T., Hamer Rogotner, S., Silman, I., Leader, H., Ashani, Y., Goldsmith, M., Greisen, P., Tawfik, D., Sussman, L.J.

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Funding Organization	Location	Grant Number
DTRA	United States	HDTRA1-11-C-0026).
DTRA	United States	CB10265 / HDTRA1724528

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description