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- PDB-5z5j: Crystal structure of a lactonase double mutant -

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Basic information

Entry
Database: PDB / ID: 5z5j
TitleCrystal structure of a lactonase double mutant
ComponentsLactonase for protein
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesRhinocladiella mackenziei CBS 650.93 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsZheng, Y.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400678, 31470240, 31500642, 31570130, 31600058, and 31600638 China
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
DepositionJan 18, 2018Deposition 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

Downloads & links

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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)233,3459
Polymers233,2398
Non-polymers1061
Water25,1131394
1
A: Lactonase for protein
C: Lactonase for protein


Theoretical massNumber of molelcules
Total (without water)58,3102
Polymers58,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area20340 Å2
MethodPISA
2
B: Lactonase for protein
D: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4163
Polymers58,3102
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-8 kcal/mol
Surface area20470 Å2
MethodPISA
3
E: Lactonase for protein
H: Lactonase for protein


Theoretical massNumber of molelcules
Total (without water)58,3102
Polymers58,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-12 kcal/mol
Surface area20020 Å2
MethodPISA
4
F: Lactonase for protein
G: Lactonase for protein


Theoretical massNumber of molelcules
Total (without water)58,3102
Polymers58,3102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-12 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.379, 94.969, 100.500
Angle α, β, γ (deg.)90.71, 92.11, 91.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lactonase for protein


Mass: 29154.854 Da / Num. of mol.: 8 / Fragment: UNP residues 3-266 / Mutation: S105A, Y160A
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1394 / 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: 3.08 Å3/Da / Density % sol: 60.07 % / Mosaicity: 1.672 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.085M 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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 2, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→25 Å / Num. obs: 143209 / % possible obs: 96.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.9
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.482 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IE4

5ie4


Resolution: 2.15→24.7 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.23
RfactorNum. reflection% reflection
Rfree0.211 2023 1.41 %
Rwork0.171 --
obs0.171 143070 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16359 0 7 1394 17760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816839
X-RAY DIFFRACTIONf_angle_d0.94723002
X-RAY DIFFRACTIONf_dihedral_angle_d11.6410046
X-RAY DIFFRACTIONf_chiral_restr0.0552519
X-RAY DIFFRACTIONf_plane_restr0.0073005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1512-2.22810.29491620.230511546X-RAY DIFFRACTION78
2.2281-2.31720.27172110.223614074X-RAY DIFFRACTION94
2.3172-2.42260.22242000.203414092X-RAY DIFFRACTION95
2.4226-2.55020.24392080.208814171X-RAY DIFFRACTION95
2.5502-2.70980.25241970.199114282X-RAY DIFFRACTION96
2.7098-2.91870.24432110.194314384X-RAY DIFFRACTION97
2.9187-3.21190.25462150.184714394X-RAY DIFFRACTION97
3.2119-3.67530.19781970.168714633X-RAY DIFFRACTION98
3.6753-4.62560.16952060.134814684X-RAY DIFFRACTION99
4.6256-24.69740.17012160.141814787X-RAY DIFFRACTION99

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