5Y5V | pdb_00005y5v

Crystal structure of a novel Pyrethroid Hydrolase PytH (S78A)

• PDB DOI: https://doi.org/10.2210/pdb5Y5V/pdb

• Classification: HYDROLASE
• Organism(s): Sphingobium faniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-08-09 Released: 2018-08-15 
• Deposition Author(s): Xu, D.Q., Ran, T.T., He, J., Wang, W.W.
• Funding Organization(s): State's Key Project of Research and Development Plan, Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Structure and Catalytic Mechanism of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2

Xu, D.Q., Gao, Y.Y., Ran, T.T., Zeng, L.P., He, J., Wang, W.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 187.14 kDa 
• Atom Count: 11,233 
• Modelled Residue Count: 1,505 
• Deposited Residue Count: 1,728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrethroid hydrolase	A, B, C, D, E, F	288	Sphingobium faniae	Mutation(s): 1  Gene Names: pytH
UniProt
Find proteins for D0VUS3 (Sphingobium faniae) Explore D0VUS3  Go to UniProtKB:  D0VUS3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.2	α = 90
b = 168.2	β = 90
c = 123.626	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Xu, D.Q., Ran, T.T., He, J., Wang, W.W.

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Funding Organization	Location	Grant Number
State's Key Project of Research and Development Plan	China	2016YFD0801102
Natural Science Foundation of China	China	31400055

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary