6FQE | pdb_00006fqe

Phosphotriesterase PTE_A53_4

• PDB DOI: https://doi.org/10.2210/pdb6FQE/pdb

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


• Deposited: 2018-02-14 Released: 2019-03-13 
• 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: 
  0.186 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Phosphotriesterase PTE_A53_4

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.

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: 74.27 kDa 
• Atom Count: 5,579 
• Modeled Residue Count: 667 
• Deposited Residue Count: 680 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathion hydrolase	A	340	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathion hydrolase	B	340	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D6K (Subject of Investigation/LOI)	F [auth A], K [auth B]	(4~{S},6~{R})-2,2,6-trimethyl-1,3-dioxan-4-ol C7 H14 O3 YZGBOJCVSXYSKT-RITPCOANSA-N
PEG (Subject of Investigation/LOI)	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	C [auth A], H [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:  0.186 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.55	α = 90
b = 81.3	β = 94.96
c = 70.61	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: 2019-03-13 
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: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description