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- PDB-3wzl: ZEN lactonase -

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Basic information

Entry
Database: PDB / ID: 3wzl
TitleZEN lactonase
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / alpha/beta-hydrolase / lactonase / zearalenone
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / response to toxic substance / hydrolase activity
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKo, T.P. / Huang, C.H. / Liu, J.R. / Guo, R.T.
CitationJournal: RSC ADV / Year: 2014
Title: Crystal structure and substrate-binding mode of the mycoestrogen-detoxifying lactonase ZHD from Clonostachys rosea
Authors: Peng, W. / Ko, T.P. / Yang, Y. / Zheng, Y. / Chen, C.C. / Zhu, Z. / Huang, C.H. / Zeng, Y.F. / Huang, J.W. / Wand, A.H.-J. / Liu, J.R. / Guo, R.T.
History
DepositionOct 1, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)91,4953
Polymers91,4953
Non-polymers00
Water4,234235
1
A: Zearalenone hydrolase
B: Zearalenone hydrolase


Theoretical massNumber of molelcules
Total (without water)60,9972
Polymers60,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-13 kcal/mol
Surface area20480 Å2
MethodPISA
2
C: Zearalenone hydrolase

C: Zearalenone hydrolase


Theoretical massNumber of molelcules
Total (without water)60,9972
Polymers60,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1240 Å2
ΔGint-11 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.637, 86.637, 474.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-387-

HOH

31C-309-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B

NCS domain segments:

Component-ID: 1 / 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: 5 / Auth seq-ID: 1 - 264 / Label seq-ID: 15 - 278

Dom-IDAuth asym-IDLabel asym-ID
1CC
2AA
3BB

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Components

#1: Protein Zearalenone hydrolase


Mass: 30498.426 Da / Num. of mol.: 3
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) / References: UniProt: Q8NKB0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 2000 MME, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 34045 / Num. obs: 33747 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 37.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.9 / % possible all: 92.2

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→24.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 22.924 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.567 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26632 1635 5 %RANDOM
Rwork0.20992 ---
all0.21266 33863 --
obs0.21266 31238 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.316 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å22.02 Å20 Å2
2--4.05 Å20 Å2
3----6.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 0 235 6301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226219
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9588496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78324.096249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55915978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4091530
X-RAY DIFFRACTIONr_chiral_restr0.110.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214719
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.861.53957
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6426423
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34732262
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9044.52073
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C1056MEDIUM POSITIONAL0.390.5
2A1056MEDIUM POSITIONAL0.230.5
3B1056MEDIUM POSITIONAL0.240.5
1C966LOOSE POSITIONAL0.695
2A966LOOSE POSITIONAL0.465
3B966LOOSE POSITIONAL0.535
1C1056MEDIUM THERMAL32.42
2A1056MEDIUM THERMAL16.792
3B1056MEDIUM THERMAL16.362
1C966LOOSE THERMAL31.5110
2A966LOOSE THERMAL16.3410
3B966LOOSE THERMAL16.0510
LS refinement shellResolution: 2.597→2.736 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.33 186
Rwork0.281 3907
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)
10.6505-0.0109-0.17850.126-0.00971.8377-0.16110.11-0.02090.13560.18470.0033-0.05530.0357-0.02350.54090.07270.03360.2679-0.02230.2894-17.709118.157911.3335
20.31720.287-0.47790.3318-0.19081.8870.01910.0852-0.05020.0360.1162-0.0384-0.1346-0.0468-0.13530.4443-0.23470.04580.3221-0.02010.3051-7.961526.1668-27.5081
31.3652-1.2193-0.98691.17680.46144.8260.06070.0251-0.4938-0.13710.12880.47180.1113-0.9287-0.18950.1065-0.185-0.20090.44260.41561.237-49.1473.5492-19.8835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 264
2X-RAY DIFFRACTION2B1 - 264
3X-RAY DIFFRACTION3C1 - 264

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