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- PDB-8cln: Zearalenone lactonase from Streptomyces coelicoflavus, SeMet deri... -

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Basic information

Entry
Database: PDB / ID: 8cln
TitleZearalenone lactonase from Streptomyces coelicoflavus, SeMet derivative for SAD phasing
ComponentsHydrolase
KeywordsHYDROLASE / zearalenone / mycotoxin / lactonase / carboxylesterase / esterase / biodegradation / SeMet / Selenomethionine
Function / homology:
Function and homology information
Biological speciesStreptomyces coelicoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
C: Hydrolase
D: Hydrolase


Theoretical massNumber of molelcules
Total (without water)139,3574
Polymers139,3574
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-3 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.386, 75.386, 404.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Hydrolase


Mass: 34839.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicoflavus (bacteria) / Gene: SMCF_1294 / Production host: Escherichia coli (E. coli) / References: UniProt: H1Q8U7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.02M CaCl2, 0.1M NaAcetate 4.6, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.5→46.91 Å / Num. obs: 47746 / % possible obs: 99.94 % / Redundancy: 19.2 % / Biso Wilson estimate: 20.75 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1202 / Rpim(I) all: 0.0282 / Rrim(I) all: 0.1235 / Net I/σ(I): 20.75
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.7228 / Mean I/σ(I) obs: 4.86 / Num. unique obs: 4683 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.1703 / Rrim(I) all: 0.7429 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4489refinement
XDSdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.91 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 3707 4.17 %
Rwork0.1831 --
obs0.1853 47730 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9373 0 0 38 9411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049663
X-RAY DIFFRACTIONf_angle_d0.71913179
X-RAY DIFFRACTIONf_dihedral_angle_d5.6161329
X-RAY DIFFRACTIONf_chiral_restr0.0431384
X-RAY DIFFRACTIONf_plane_restr0.0131744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.27231420.25053263X-RAY DIFFRACTION100
2.53-2.570.27181460.24693268X-RAY DIFFRACTION100
2.57-2.60.27891500.23173356X-RAY DIFFRACTION100
2.6-2.640.33591340.233163X-RAY DIFFRACTION100
2.64-2.680.30881500.22743355X-RAY DIFFRACTION100
2.68-2.730.24181380.21993230X-RAY DIFFRACTION100
2.73-2.780.31881430.21833356X-RAY DIFFRACTION100
2.78-2.830.24841380.20993162X-RAY DIFFRACTION100
2.83-2.880.28911460.20963345X-RAY DIFFRACTION100
2.88-2.940.27541480.20753246X-RAY DIFFRACTION100
2.94-30.25241480.21373289X-RAY DIFFRACTION100
3-3.070.27411440.22983256X-RAY DIFFRACTION100
3.07-3.150.26951380.20833312X-RAY DIFFRACTION100
3.15-3.230.24151380.19373257X-RAY DIFFRACTION100
3.23-3.330.30491390.20043292X-RAY DIFFRACTION100
3.33-3.440.23271480.19113348X-RAY DIFFRACTION100
3.44-3.560.22231320.1833232X-RAY DIFFRACTION100
3.56-3.70.23981500.18083240X-RAY DIFFRACTION100
3.7-3.870.21821380.17663269X-RAY DIFFRACTION100
3.87-4.070.23531480.15953299X-RAY DIFFRACTION100
4.08-4.330.18241460.14843292X-RAY DIFFRACTION100
4.33-4.660.22471320.14553313X-RAY DIFFRACTION100
4.66-5.130.19671440.15623245X-RAY DIFFRACTION100
5.13-5.870.20571440.17173308X-RAY DIFFRACTION100
5.88-7.390.21571350.19563270X-RAY DIFFRACTION100
7.4-46.910.18841480.16123268X-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)
10.8401-0.0667-0.21220.9560.15941.96470.03640.01920.01830.19710.0083-0.0644-0.08120.1274-0.0380.27390.0653-0.01030.256-0.0150.278835.00376.052858.9055
21.24440.06980.01121.3509-0.2851.6071-0.00930.2272-0.1902-0.08110.0660.12660.481-0.323-0.04650.3916-0.0592-0.010.3039-0.06140.326723.4185-21.575642.4529
30.81040.0844-0.221.7157-0.30931.5794-0.02360.2530.1268-0.22860.17670.1571-0.2327-0.2339-0.14990.3634-0.00640.00290.51250.05560.254628.014516.964517.9418
40.86420.1413-0.45971.3226-0.13322.0631-0.050.1804-0.0576-0.28710.1744-0.37050.07480.412-0.08240.3435-0.01620.07180.6265-0.14760.368454.9442-4.181818.988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 307)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 308)
3X-RAY DIFFRACTION3(chain 'C' and resid 9 through 307)
4X-RAY DIFFRACTION4(chain 'D' and resid 10 through 308)

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