5Y5R | pdb_00005y5r

Crystal structure of a novel Pyrethroid Hydrolase PytH with BIF

PDB DOI: https://doi.org/10.2210/pdb5Y5R/pdb

Classification: HYDROLASE
Organism(s): Sphingobium faniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-09 Released: 2018-08-15
Deposition Author(s): Xu, D.Q., Ran, T.T., Wang, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.322 (Depositor), 0.324 (DCC)
R-Value Work:
0.273 (Depositor), 0.277 (DCC)
R-Value Observed:
0.276 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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., Ran, T.T., He, J., Wang, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 191.74 kDa
Atom Count: 12,042
Modeled Residue Count: 1,511
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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): 0 Gene Names: pytH
UniProt
Find proteins for D0VUS3 (Sphingobium faniae) Explore D0VUS3 Go to UniProtKB: D0VUS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VUS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8NL Query on 8NL Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	(2-methyl-3-phenyl-phenyl)methyl (1~{S})-3-[(~{E})-2-chloranyl-3,3,3-tris(fluoranyl)prop-1-enyl]-2,2-dimethyl-cyclopropane-1-carboxylate C₂₃ H₂₂ Cl F₃ O₂ OMFRMAHOUUJSGP-AZUAARDMSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.322 (Depositor), 0.324 (DCC)
R-Value Work: 0.273 (Depositor), 0.277 (DCC)
R-Value Observed: 0.276 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.857	α = 90
b = 168.857	β = 90
c = 123.864	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-15

Deposition Author(s):

Xu, D.Q.

Ran, T.T.

Wang, W.W.

Revision History (Full details and data files)

Version 1.0: 2018-08-15
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary

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Crystal structure of a novel Pyrethroid Hydrolase PytH with BIF

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations