5WCQ

Phosphotriesterase variant S2

• PDB DOI: https://doi.org/10.2210/pdb5WCQ/pdb

• Classification: HYDROLASE
• Organism(s): Brevundimonas diminuta
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-01 Released: 2018-07-04 
• Deposition Author(s): Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.193 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Phosphotriesterase variant S2

Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

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)

Macromolecule Content

• Total Structure Weight: 73.24 kDa 
• Atom Count: 5,748 
• Modelled Residue Count: 643 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A, B [auth G]	333	Brevundimonas diminuta	Mutation(s): 0
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
CAC	E [auth A], L [auth G]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
MPD	F [auth A], G [auth A], H [auth A], I [auth A], M [auth G], N [auth G], O [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	C [auth A], D [auth A], J [auth G], K [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B [auth G]	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.193 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.233	α = 90
b = 85.476	β = 90
c = 88.215	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2023-04-26
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection