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- PDB-8clo: Zearalenone lactonase from Streptomyces coelicoflavus -

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Basic information

Entry
Database: PDB / ID: 8clo
TitleZearalenone lactonase from Streptomyces coelicoflavus
ComponentsHydrolase
KeywordsHYDROLASE / zearalenone / mycotoxin / lactonase / carboxylesterase / esterase / biodegradation / streptomyces coelicoflavus
Function / homology:
Function and homology information
Biological speciesStreptomyces coelicoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPuehringer, D. / Grishkovskaya, I. / Mlynek, G. / Kostan, J.
Funding support Austria, Czech Republic, 5items
OrganizationGrant numberCountry
Christian Doppler ForschungsgesellschaftFA743017 Austria
Austrian Research Promotion AgencyLaura Bassi Center for Optimised Structural Studies Austria
Ministry of Education (MoE, Czech Republic)INBIO - CZ.02.1.01/0.0/0.0/16_026/0008451 Czech Republic
Ministry of Education (MoE, Czech Republic)RECETOX RI LM2018121 Czech Republic
Ministry of Education (MoE, Czech Republic)ELIXIR - LM201813 Czech Republic
CitationJournal: Acs Catalysis / Year: 2024
Title: Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone.
Authors: Fruhauf, S. / Puhringer, D. / Thamhesl, M. / Fajtl, P. / Kunz-Vekiru, E. / Hobartner-Gussl, A. / Schatzmayr, G. / Adam, G. / Damborsky, J. / Djinovic-Carugo, K. / Prokop, Z. / Moll, W.D.
History
DepositionFeb 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,42314
Polymers69,6782
Non-polymers74512
Water6,864381
1
A: Hydrolase
B: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,84628
Polymers139,3574
Non-polymers1,49024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)173.548, 69.297, 64.423
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21A-643-

HOH

31B-540-

HOH

41B-634-

HOH

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Components

#1: Protein Hydrolase


Mass: 34839.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicoflavus (bacteria) / Gene: SMCF_1294 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H1Q8U7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Imidazole / MES pH 6.5, 0.06 M MgCl2, CaCl2, 30% w/v {40% ethylene glycol, 20% PEG 8000}

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.4→46.31 Å / Num. obs: 148595 / % possible obs: 99.52 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.26 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.06537 / Rrim(I) all: 0.137 / Net I/σ(I): 6.18
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.534 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 14556 / CC1/2: 0.298 / CC star: 0.678 / Rpim(I) all: 0.9222 / Rrim(I) all: 1.801 / % possible all: 97.86

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4489refinement
XDSdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.31 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 2000 1.35 %
Rwork0.1867 --
obs0.1871 148542 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 48 381 5205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095022
X-RAY DIFFRACTIONf_angle_d1.0146839
X-RAY DIFFRACTIONf_dihedral_angle_d6.164710
X-RAY DIFFRACTIONf_chiral_restr0.078722
X-RAY DIFFRACTIONf_plane_restr0.014902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.37521390.334610242X-RAY DIFFRACTION98
1.44-1.470.34121420.297610354X-RAY DIFFRACTION99
1.47-1.520.31671420.268310370X-RAY DIFFRACTION100
1.52-1.570.29771430.243210475X-RAY DIFFRACTION100
1.57-1.620.30271420.233110436X-RAY DIFFRACTION100
1.62-1.690.25611430.216710472X-RAY DIFFRACTION100
1.69-1.760.28571420.203610462X-RAY DIFFRACTION100
1.76-1.860.27121440.184710492X-RAY DIFFRACTION100
1.86-1.970.22211430.161610501X-RAY DIFFRACTION100
1.97-2.130.18451430.160210463X-RAY DIFFRACTION100
2.13-2.340.18931430.158510489X-RAY DIFFRACTION100
2.34-2.680.19091440.161110528X-RAY DIFFRACTION100
2.68-3.370.17091440.172510556X-RAY DIFFRACTION100
3.37-46.310.20081460.18810702X-RAY DIFFRACTION100

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