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- PDB-5ie4: Crystal structure of a lactonase mutant in complex with substrate a -

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Basic information

Entry
Database: PDB / ID: 5ie4
TitleCrystal structure of a lactonase mutant in complex with substrate a
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE
Function / homology: / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / response to toxic substance / Alpha/Beta hydrolase fold / hydrolase activity / Chem-36J / Zearalenone hydrolase
Function and homology information
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsZheng, Y.Y. / Xu, Z.X. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Acs Catalysis / Year: 2016
Title: Enhanced alph-Zearalenol Hydrolyzing Activity of a Mycoestrogen-Detoxifying Lactonase by Structure-Based Engineering
Authors: Xu, Z.X. / Liu, W.D. / Chen, C.C. / Li, Q. / Huang, J.W. / Ko, T.P. / Liu, G. / Liu, W. / Peng, W. / Cheng, Y.S. / Chen, Y. / Jin, J. / Li, H. / Zheng, Y.Y. / Guo, R.T.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zearalenone hydrolase
B: Zearalenone hydrolase
C: Zearalenone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9295
Polymers86,2883
Non-polymers6412
Water3,603200
1
A: Zearalenone hydrolase
B: Zearalenone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1664
Polymers57,5252
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-13 kcal/mol
Surface area20150 Å2
MethodPISA
2
C: Zearalenone hydrolase

C: Zearalenone hydrolase


Theoretical massNumber of molelcules
Total (without water)57,5252
Polymers57,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1080 Å2
ΔGint-9 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.205, 86.205, 473.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 264 / Label seq-ID: 1 - 264

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Zearalenone hydrolase / lactonase


Mass: 28762.627 Da / Num. of mol.: 3 / Mutation: S102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonostachys rosea (fungus) / Gene: zhd101 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NKB0
#2: Chemical ChemComp-36J / (3S,7R,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one


Mass: 320.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.94 Å3/Da / Density % sol: 58.18 % / Mosaicity: 0.613 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 2000 MME, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 26370 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Χ2: 1.205 / Net I/av σ(I): 36.758 / Net I/σ(I): 13.9 / Num. measured all: 162671
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.96.30.163198.9
2.9-3.026.40.136198.5
3.02-3.156.40.106198
3.15-3.326.30.088198.3
3.32-3.536.30.072198.7
3.53-3.86.20.061198.5
3.8-4.186.20.053198
4.18-4.786.10.044197.4
4.78-6.0160.043196.8
6.01-255.50.026192.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZL

3wzl


Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.875 / SU B: 22.212 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.751 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26483 1264 4.8 %RANDOM
Rwork0.20334 ---
obs0.2063 25085 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.008 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 46 202 5447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195371
X-RAY DIFFRACTIONr_bond_other_d0.0030.025054
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9667321
X-RAY DIFFRACTIONr_angle_other_deg0.9693.00311660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2565665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98324.038213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.65315828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2921525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0215961
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021150
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_it3.8323.5072701
X-RAY DIFFRACTIONr_mcbond_other3.8323.5062700
X-RAY DIFFRACTIONr_mcangle_it6.0165.2313353
X-RAY DIFFRACTIONr_mcangle_other6.0155.2323354
X-RAY DIFFRACTIONr_scbond_it3.4993.7032669
X-RAY DIFFRACTIONr_scbond_other3.4973.7032669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4945.4693969
X-RAY DIFFRACTIONr_long_range_B_refined8.69428.0196147
X-RAY DIFFRACTIONr_long_range_B_other8.69728.0056139
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 30162 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 86 -
Rwork0.269 1822 -
obs--98.35 %

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