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- PDB-3wzm: ZEN lactonase mutant complex -

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Basic information

Entry
Database: PDB / ID: 3wzm
TitleZEN lactonase mutant complex
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
Chem-ZER / Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)92,4026
Polymers91,4473
Non-polymers9553
Water7,674426
1
A: Zearalenone hydrolase
B: Zearalenone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6024
Polymers60,9652
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-13 kcal/mol
Surface area20050 Å2
MethodPISA
2
C: Zearalenone hydrolase
hetero molecules

C: Zearalenone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6024
Polymers60,9652
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)86.842, 86.842, 471.784
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
11C-424-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
12C
22A
32B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU5CC1 - 26415 - 278
21METMETLEULEU5AA1 - 26415 - 278
31METMETLEULEU5BB1 - 26415 - 278
12ZERZERZERZER1CF300
22ZERZERZERZER1AD300
32ZERZERZERZER1BE300

NCS ensembles :
ID
1
2

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Components

#1: Protein Zearalenone hydrolase


Mass: 30482.430 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) / References: UniProt: Q8NKB0
#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.: 3 / Source method: obtained synthetically / Formula: C18H22O5 / Comment: toxin*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 56.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 2000 MME, 0.1M Bis-Tris pH 6.5, Soaking with Reservoir + 10mM zearalenone) , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 21, 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: 2.48→20 Å / Num. all: 38853 / Num. obs: 38626 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 34
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 6.2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3WZL

3wzl


Resolution: 2.48→19.95 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.529 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26788 1848 5 %RANDOM
Rwork0.20421 ---
all0.20736 38778 --
obs0.20736 35113 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.646 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å21.16 Å20 Å2
2--2.31 Å20 Å2
3----3.47 Å2
Refinement stepCycle: LAST / Resolution: 2.48→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 69 426 6558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226288
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9698589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62124.096249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15915975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4841530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214785
X-RAY DIFFRACTIONr_mcbond_it0.871.53957
X-RAY DIFFRACTIONr_mcangle_it1.60426420
X-RAY DIFFRACTIONr_scbond_it2.34732331
X-RAY DIFFRACTIONr_scangle_it3.7584.52169
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C1056MEDIUM POSITIONAL0.320.5
12A1056MEDIUM POSITIONAL0.180.5
13B1056MEDIUM POSITIONAL0.220.5
11C988LOOSE POSITIONAL0.555
12A988LOOSE POSITIONAL0.385
13B988LOOSE POSITIONAL0.485
11C1056MEDIUM THERMAL27.132
12A1056MEDIUM THERMAL14.892
13B1056MEDIUM THERMAL132
11C988LOOSE THERMAL26.2110
12A988LOOSE THERMAL14.3410
13B988LOOSE THERMAL12.7610
21C23TIGHT POSITIONAL0.040.05
22A23TIGHT POSITIONAL0.040.05
23B23TIGHT POSITIONAL0.030.05
21C23TIGHT THERMAL3.90.5
22A23TIGHT THERMAL2.010.5
23B23TIGHT THERMAL1.910.5
LS refinement shellResolution: 2.482→2.614 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.311 257
Rwork0.242 4628
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)
10.8340.2496-0.13440.6581-0.0082.1814-0.1210.0665-0.00330.13390.1979-0.0138-0.08330.0792-0.07690.35720.0340.02020.1672-0.02520.2432-17.890518.295611.0766
20.92980.3216-0.72410.6643-0.40662.7931-0.01550.10080.02030.05150.1017-0.0735-0.0885-0.1098-0.08620.3023-0.130.02330.2102-0.01710.2311-7.944326.3094-27.3866
32.0824-1.1274-0.25180.89820.98424.4659-0.02630.116-0.3881-0.04880.00920.2780.0776-0.60390.01710.0767-0.1433-0.13460.3250.1820.6359-48.99733.4387-19.9495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 300
2X-RAY DIFFRACTION2B1 - 300
3X-RAY DIFFRACTION3C1 - 300

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