5Z97 | pdb_00005z97

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 (Depositor), 0.268 (DCC)
R-Value Work:
0.210 (Depositor), 0.217 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 1,050
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] Interactions & Density 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] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.266 (Depositor), 0.268 (DCC)
R-Value Work: 0.210 (Depositor), 0.217 (DCC)
R-Value Observed: 0.212 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.