5Z5J

Crystal structure of a lactonase double mutant

PDB DOI: https://doi.org/10.2210/pdb5Z5J/pdb

Classification: HYDROLASE
Organism(s): Rhinocladiella mackenziei CBS 650.93
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-01-18 Released: 2018-05-02
Deposition Author(s): Zheng, Y.Y., Liu, W.D., Chen, C.C., Guo, R.T.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Mycoestrogen-Detoxifying Lactonase from Rhinocladiella mackenziei: Molecular Insight into ZHD Substrate Selectivity

Zheng, Y.Y., Liu, W.T., Chen, C.C., Hu, X.Y., Liu, W.D., Ko, T.P., Tang, X.K., Wei, H.L., Huang, J.W., Guo, R.T.

(2018) ACS Catal 8: 4294-4298

DOI: https://doi.org/10.1021/acscatal.8b00464

Macromolecule Content

Total Structure Weight: 233.34 kDa
Atom Count: 17,760
Modelled Residue Count: 2,102
Deposited Residue Count: 2,112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactonase for protein	A, B, C, D, E A, B, C, D, E, F, G, H	264	Rhinocladiella mackenziei CBS 650.93	Mutation(s): 2 Gene Names: Z518_04590
UniProt
Find proteins for A0A0D2ILK1 (Rhinocladiella mackenziei CBS 650.93) Explore A0A0D2ILK1 Go to UniProtKB: A0A0D2ILK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D2ILK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.171
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.379	α = 90.71
b = 94.969	β = 92.11
c = 100.5	γ = 91.91

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31400678, 31470240, 31500642, 31570130, 31600058, and 31600638

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.