5Z97

Crystal structure of a lactonase double mutant in complex with ligand N

PDB DOI: https://doi.org/10.2210/pdb5Z97/pdb

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

Deposited: 2018-02-02 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: 2.32 Å
R-Value Free: 0.266
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 117.39 kDa
Atom Count: 8,498
Modelled Residue Count: 1,050
Deposited Residue Count: 1,052
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	263	Rhinocladiella mackenziei CBS 650.93	Mutation(s): 2
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZER Query on ZER Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C]	E [auth A], G [auth B], H [auth C]	(3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione C₁₈ H₂₂ O₅ MBMQEIFVQACCCH-QBODLPLBSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.266
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.319	α = 90
b = 110.52	β = 99.93
c = 127.779	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.