3WZM | pdb_00003wzm

ZEN lactonase mutant complex

PDB DOI: https://doi.org/10.2210/pdb3WZM/pdb

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

Deposited: 2014-10-01 Released: 2014-11-26
Deposition Author(s): Ko, T.P., Huang, C.H., Liu, J.R., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.268 (Depositor), 0.258 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure and substrate-binding mode of the mycoestrogen-detoxifying lactonase ZHD from Clonostachys rosea

Peng, W., Ko, T.P., Yang, Y., Zheng, Y., Chen, C.C., Zhu, Z., Huang, C.H., Zeng, Y.F., Huang, J.W., Wand, A.H.-J., Liu, J.R., Guo, R.T.

(2014) RSC Adv 4: 62321-62325

DOI: https://doi.org/10.1039/c4ra12111b

Macromolecule Content

Total Structure Weight: 92.4 kDa
Atom Count: 6,558
Modeled Residue Count: 792
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zearalenone hydrolase	A, B, C	278	Clonostachys rosea	Mutation(s): 1 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
ZER Query on ZER Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [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 D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.268 (Depositor), 0.258 (DCC)
R-Value Work: 0.204 (Depositor), 0.200 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.842	α = 90
b = 86.842	β = 90
c = 471.784	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.