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- PDB-8clv: Zearalenone lactonase of Rhodococcus erythropolis in complex with... -

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Basic information

Entry
Database: PDB / ID: 8clv
TitleZearalenone lactonase of Rhodococcus erythropolis in complex with hydrolyzed zearalenone
ComponentsZearalenone lactonase
KeywordsHYDROLASE / zearalenone / mycotoxin / lactonase / carboxylesterase / esterase / biodegradation / Rhodococcus erythropolis / hydrolyzed zearalenone / hzen
Function / homologyChem-ZGR
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)149,4798
Polymers148,1344
Non-polymers1,3464
Water2,432135
1
A: Zearalenone lactonase
B: Zearalenone lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7404
Polymers74,0672
Non-polymers6732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Zearalenone lactonase
D: Zearalenone lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7404
Polymers74,0672
Non-polymers6732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.380, 172.090, 136.130
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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-ZGR / 2,4-dihydroxy-6-[(1E,10S)-10-hydroxy-6-oxoundec-1-en-1-yl]benzoic acid


Mass: 336.380 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.54→47.05 Å / Num. obs: 44439 / % possible obs: 92.26 % / Redundancy: 10.5 % / Biso Wilson estimate: 47.85 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2197 / Rpim(I) all: 0.069 / Rrim(I) all: 0.2309 / Net I/σ(I): 9.63
Reflection shellResolution: 2.54→2.631 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.984 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4434 / CC1/2: 0.221 / Rpim(I) all: 0.652 / Rrim(I) all: 2.096 / % possible all: 92.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4489refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→47.05 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1999 4.51 %
Rwork0.2139 --
obs0.2154 44325 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9444 0 96 135 9675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039828
X-RAY DIFFRACTIONf_angle_d0.58213408
X-RAY DIFFRACTIONf_dihedral_angle_d9.3731336
X-RAY DIFFRACTIONf_chiral_restr0.041420
X-RAY DIFFRACTIONf_plane_restr0.0051768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60.36271410.34782998X-RAY DIFFRACTION93
2.6-2.670.41041420.34113014X-RAY DIFFRACTION93
2.67-2.750.39511430.33593011X-RAY DIFFRACTION93
2.75-2.840.36591420.31163012X-RAY DIFFRACTION93
2.84-2.940.32851450.28083046X-RAY DIFFRACTION94
2.94-3.060.34991440.28433052X-RAY DIFFRACTION94
3.06-3.20.31111430.26473044X-RAY DIFFRACTION93
3.2-3.370.30281430.24253034X-RAY DIFFRACTION94
3.37-3.580.28021450.22023057X-RAY DIFFRACTION93
3.58-3.860.21811430.19163023X-RAY DIFFRACTION92
3.86-4.240.18011430.16693035X-RAY DIFFRACTION92
4.24-4.860.17241420.1483007X-RAY DIFFRACTION91
4.86-6.120.18561410.16842992X-RAY DIFFRACTION90
6.12-47.050.19651420.17473001X-RAY DIFFRACTION87

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