5Y51 | pdb_00005y51

Crystal structure of PytH_H230A

PDB DOI: https://doi.org/10.2210/pdb5Y51/pdb

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

Deposited: 2017-08-06 Released: 2018-08-08
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.330 (Depositor), 0.328 (DCC)
R-Value Work:
0.269 (Depositor), 0.270 (DCC)
R-Value Observed:
0.272 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5Y51

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: 186.83 kDa
Atom Count: 11,414
Modeled Residue Count: 1,497
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: 2.30 Å
R-Value Free: 0.330 (Depositor), 0.328 (DCC)
R-Value Work: 0.269 (Depositor), 0.270 (DCC)
R-Value Observed: 0.272 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.375	α = 90
b = 168.375	β = 90
c = 123.858	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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