5IE5 | pdb_00005ie5

Crystal structure of a lactonase double mutant in complex with substrate a

PDB DOI: https://doi.org/10.2210/pdb5IE5/pdb

Classification: HYDROLASE
Organism(s): Clonostachys rosea
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-02-25 Released: 2017-01-04
Deposition Author(s): Zheng, Y.Y., Xu, Z.X., Liu, W.D., Chen, C.C., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.270 (Depositor), 0.306 (DCC)
R-Value Work:
0.214 (Depositor), 0.265 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Enhanced alph-Zearalenol Hydrolyzing Activity of a Mycoestrogen-Detoxifying Lactonase by Structure-Based Engineering

Xu, Z.X., Liu, W.D., Chen, C.C., Li, Q., Huang, J.W., Ko, T.P., Liu, G., Liu, W., Peng, W., Cheng, Y.S., Chen, Y., Jin, J., Li, H., Zheng, Y.Y., Guo, R.T.

(2016) ACS Catal 6: 7657-7663

DOI: https://doi.org/10.1021/acscatal.6b01826

Macromolecule Content

Total Structure Weight: 87.05 kDa
Atom Count: 5,648
Modeled Residue Count: 692
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zearalenone hydrolase	A, B, C	264	Clonostachys rosea	Mutation(s): 2 Gene Names: zhd101 EC: 3.1.1
UniProt
Find proteins for Q8NKB0 (Bionectria ochroleuca) Explore Q8NKB0 Go to UniProtKB: Q8NKB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NKB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
36J Query on 36J Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	(3S,7R,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one C₁₈ H₂₄ O₅ FPQFYIAXQDXNOR-QDKLYSGJSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.270 (Depositor), 0.306 (DCC)
R-Value Work: 0.214 (Depositor), 0.265 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.164	α = 90
b = 86.164	β = 90
c = 471.862	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-01-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-01-04
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-04-03
Changes: 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.