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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.291 (Depositor), 0.291 (DCC)
R-Value Work:
0.216 (Depositor), 0.228 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrethroid hydrolase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VUS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] 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		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.291 (Depositor), 0.291 (DCC)
R-Value Work: 0.216 (Depositor), 0.228 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-15

Deposition Author(s):

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 (Full details and data files)

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

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