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- PDB-8clt: Zearalenone lactonase of Rhodococcus erythropolis -

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Basic information

Entry
Database: PDB / ID: 8clt
TitleZearalenone lactonase of Rhodococcus erythropolis
ComponentsZearalenone lactonase
KeywordsHYDROLASE / zearalenone / mycotoxin / lactonase / carboxylesterase / esterase / biodegradation / Rhodococcus erythropolis
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsPuehringer, D. / Mlynek, G.
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: Zearalenone lactonase
B: Zearalenone lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43512
Polymers73,5142
Non-polymers92110
Water10,251569
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-14 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.467, 121.803, 172.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

21B-680-

HOH

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Components

#1: Protein Zearalenone lactonase


Mass: 36757.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M BIS-TRIS 5.5 pH, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.46→47.53 Å / Num. obs: 114638 / % possible obs: 92.98 % / Redundancy: 6 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1014 / Rpim(I) all: 0.04401 / Rrim(I) all: 0.1108 / Net I/σ(I): 10.2
Reflection shellResolution: 1.46→1.512 Å / Redundancy: 0.18 % / Rmerge(I) obs: 4.677 / Mean I/σ(I) obs: 0.18 / Num. unique obs: 9488 / CC1/2: 0.109 / CC star: 0.443 / Rpim(I) all: 2.872 / Rrim(I) all: 5.527 / % possible all: 39.33

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→47.53 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 1895 1.73 %
Rwork0.1644 --
obs0.165 109245 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 60 569 5415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095003
X-RAY DIFFRACTIONf_angle_d1.0146813
X-RAY DIFFRACTIONf_dihedral_angle_d7.486682
X-RAY DIFFRACTIONf_chiral_restr0.081717
X-RAY DIFFRACTIONf_plane_restr0.017895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.4459420.50252248X-RAY DIFFRACTION28
1.5-1.540.46051050.43626466X-RAY DIFFRACTION79
1.54-1.580.38781410.36687786X-RAY DIFFRACTION95
1.58-1.630.36711490.30558155X-RAY DIFFRACTION100
1.63-1.690.30651410.27468182X-RAY DIFFRACTION100
1.69-1.760.32031400.24928196X-RAY DIFFRACTION100
1.76-1.840.26171460.23838181X-RAY DIFFRACTION100
1.84-1.940.24341400.18618229X-RAY DIFFRACTION100
1.94-2.060.22121440.14938191X-RAY DIFFRACTION100
2.06-2.220.20341530.13758260X-RAY DIFFRACTION100
2.22-2.440.17011380.13658251X-RAY DIFFRACTION100
2.44-2.790.17531490.13548298X-RAY DIFFRACTION100
2.79-3.520.15791540.13738319X-RAY DIFFRACTION100
3.52-47.530.16871530.14478588X-RAY DIFFRACTION100

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