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- PDB-5xo8: Crystal structure of a novel ZEN lactonase mutant with ligand Z -

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Basic information

Entry
Database: PDB / ID: 5xo8
TitleCrystal structure of a novel ZEN lactonase mutant with ligand Z
ComponentsLactonase for protein
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-ZER / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesRhinocladiella mackenziei CBS 650.93 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZheng, Y.Y. / Liu, W.T. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Acs Catalysis / Year: 2018
Title: Crystal Structure of a Mycoestrogen-Detoxifying Lactonase from Rhinocladiella mackenziei: Molecular Insight into ZHD Substrate Selectivity
Authors: Zheng, Y.Y. / Liu, W.T. / Chen, C.C. / Hu, X.Y. / Liu, W.D. / Ko, T.P. / Tang, X.K. / Wei, H.L. / Huang, J.W. / Guo, R.T.
History
DepositionMay 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactonase for protein
B: Lactonase for protein
C: Lactonase for protein
D: Lactonase for protein
E: Lactonase for protein
F: Lactonase for protein
G: Lactonase for protein
H: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,14116
Polymers235,5948
Non-polymers2,5478
Water46,7312594
1
A: Lactonase for protein
C: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5354
Polymers58,8982
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-11 kcal/mol
Surface area19980 Å2
MethodPISA
2
B: Lactonase for protein
D: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5354
Polymers58,8982
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-10 kcal/mol
Surface area20060 Å2
MethodPISA
3
E: Lactonase for protein
H: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5354
Polymers58,8982
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-12 kcal/mol
Surface area19700 Å2
MethodPISA
4
F: Lactonase for protein
G: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5354
Polymers58,8982
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-12 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.470, 95.196, 101.663
Angle α, β, γ (deg.)90.21, 92.34, 91.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lactonase for protein


Mass: 29449.219 Da / Num. of mol.: 8 / Mutation: S105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinocladiella mackenziei CBS 650.93 (fungus)
Gene: Z518_04590 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D2ILK1
#2: Chemical
ChemComp-ZER / (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione / Zearalenone


Mass: 318.364 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H22O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2594 / 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: 3.09 Å3/Da / Density % sol: 60.26 % / Mosaicity: 0.232 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.085 M Sodium Cacodylate pH 6.5, 25-28% w/v Polyethylene Glycol 8000 and 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 16, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. obs: 224832 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.9
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.302 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZL

3wzl


Resolution: 1.88→24.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.443 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 1999 0.9 %RANDOM
Rwork0.14519 ---
obs0.14551 222748 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.828 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.88→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16430 0 184 2594 19208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01917106
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215762
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.9723368
X-RAY DIFFRACTIONr_angle_other_deg1.2673.00336464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.752100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77923.604738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.164152610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.77515104
X-RAY DIFFRACTIONr_chiral_restr0.1320.22530
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02119282
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023774
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5292.4838412
X-RAY DIFFRACTIONr_mcbond_other2.5272.4838411
X-RAY DIFFRACTIONr_mcangle_it3.1243.71110502
X-RAY DIFFRACTIONr_mcangle_other3.1253.71110503
X-RAY DIFFRACTIONr_scbond_it3.5212.828694
X-RAY DIFFRACTIONr_scbond_other3.5222.828695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1054.09412865
X-RAY DIFFRACTIONr_long_range_B_refined7.13122.82722664
X-RAY DIFFRACTIONr_long_range_B_other7.07122.66322422
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 150 -
Rwork0.207 16092 -
obs--96.2 %

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