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- PDB-8clu: Zearalenone lactonase from Rhodococcus erythropolis in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8clu
TitleZearalenone lactonase from Rhodococcus erythropolis in complex with zearalactamenone
ComponentsZearalenone lactonase
KeywordsHYDROLASE / zearalenone / mycotoxin / lactonase / carboxylesterase / esterase / biodegradation / Rhodococcus erythropolis / zearalactamenone
Function / homology:
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPuehringer, D.
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

Downloads & links

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Assembly

Deposited unit
A: Zearalenone lactonase
B: Zearalenone lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7945
Polymers74,0672
Non-polymers7273
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-5 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.556, 121.840, 172.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Zearalenone lactonase


Mass: 37033.477 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-V0F / (4~{S})-4-methyl-16,18-bis(oxidanyl)-3-azabicyclo[12.4.0]octadeca-1(18),12,14,16-tetraene-2,8-dione


Mass: 317.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.58 %
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: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→47.59 Å / Num. obs: 63294 / % possible obs: 99.85 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.06529 / Rrim(I) all: 0.1713 / Net I/σ(I): 8.87
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 6.9 % / Rmerge(I) obs: 3.112 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6223 / CC1/2: 0.231 / CC star: 0.612 / Rpim(I) all: 1.26 / Rrim(I) all: 3.362 / % possible all: 99.42

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.59 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 3139 4.96 %
Rwork0.165 --
obs0.1667 63294 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 52 379 5253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015082
X-RAY DIFFRACTIONf_angle_d1.1266937
X-RAY DIFFRACTIONf_dihedral_angle_d8.705699
X-RAY DIFFRACTIONf_chiral_restr0.058727
X-RAY DIFFRACTIONf_plane_restr0.012917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.34071310.27342622X-RAY DIFFRACTION97
1.83-1.860.2891130.26112738X-RAY DIFFRACTION100
1.86-1.890.28271500.25542694X-RAY DIFFRACTION100
1.89-1.920.32051260.23992727X-RAY DIFFRACTION100
1.92-1.960.28541280.22372726X-RAY DIFFRACTION100
1.96-20.27871480.20172691X-RAY DIFFRACTION100
2-2.040.23061430.1972733X-RAY DIFFRACTION100
2.04-2.090.2131370.18242724X-RAY DIFFRACTION100
2.09-2.140.19251380.18152700X-RAY DIFFRACTION100
2.14-2.20.21971330.17662724X-RAY DIFFRACTION100
2.2-2.270.22081170.17332753X-RAY DIFFRACTION100
2.27-2.340.22321310.16122723X-RAY DIFFRACTION100
2.34-2.420.1921460.16362731X-RAY DIFFRACTION100
2.42-2.520.18871560.15582709X-RAY DIFFRACTION100
2.52-2.640.21381500.15612727X-RAY DIFFRACTION100
2.64-2.770.19111720.152737X-RAY DIFFRACTION100
2.77-2.950.19671700.14842708X-RAY DIFFRACTION100
2.95-3.180.20151670.15952722X-RAY DIFFRACTION100
3.18-3.50.19061290.14872775X-RAY DIFFRACTION100
3.5-40.17011160.13842816X-RAY DIFFRACTION100
4-5.040.14761730.1232775X-RAY DIFFRACTION100
5.04-47.590.18061650.18022913X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.556-0.03680.00691.05810.08150.9348-0.03410.04060.04390.03650.0078-0.0333-0.07030.03610.02450.2116-0.0255-0.01110.1830.00640.19721.645115.55422.8444
20.574-0.13940.04431.0284-0.08771.1595-0.02680.0384-0.03340.00780.02880.08320.0876-0.1019-0.00280.214-0.03080.00550.19740.01490.20457.6098-15.689920.2094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 332)
2X-RAY DIFFRACTION2(chain 'B' and resid 21 through 326)

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