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- PDB-6jrc: ZHD complex with hydrolyzed alpha-ZOL -

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Basic information

Entry
Database: PDB / ID: 6jrc
TitleZHD complex with hydrolyzed alpha-ZOL
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / LACTONASE / ALPHA-BETA FOLD / ZEARALENONE DEGRADE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-C3L / : / Zearalenone lactonase
Function and homology information
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHu, X.J.
CitationJournal: To Be Published
Title: Structure of ZHD complex
Authors: Hu, X.J. / Zhou, H.J. / Li, L.
History
DepositionApr 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: 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: Zearalenone hydrolase
B: Zearalenone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,34512
Polymers62,0382
Non-polymers1,30810
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.575, 89.887, 112.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zearalenone hydrolase


Mass: 31018.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonostachys rosea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9XBU7*PLUS
#2: Chemical ChemComp-C3L / 2-[(~{E},6~{R},10~{S})-6,10-bis(oxidanyl)undec-1-enyl]-4,6-bis(oxidanyl)benzoic acid


Mass: 338.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium phosphate, imidazole, potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 91757 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.984 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Net I/σ(I): 37.9
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 4516 / CC1/2: 0.939 / Rpim(I) all: 0.18 / Rrim(I) all: 0.666

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c8z

5c8z


Resolution: 1.65→35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.098 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1571 4651 5.1 %RANDOM
Rwork0.13995 ---
obs0.14084 87021 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-0 Å2
2--0.69 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 86 427 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174036
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.6536128
X-RAY DIFFRACTIONr_angle_other_deg1.6641.5829402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36222.718206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38815683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4781522
X-RAY DIFFRACTIONr_chiral_restr0.1150.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025083
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02909
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_it1.7061.7322241
X-RAY DIFFRACTIONr_mcbond_other1.7021.732240
X-RAY DIFFRACTIONr_mcangle_it2.3062.5932831
X-RAY DIFFRACTIONr_mcangle_other2.3062.5942832
X-RAY DIFFRACTIONr_scbond_it3.3332.0962232
X-RAY DIFFRACTIONr_scbond_other3.3322.0972233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.78733298
X-RAY DIFFRACTIONr_long_range_B_refined5.52922.1895190
X-RAY DIFFRACTIONr_long_range_B_other5.45521.965146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 324 -
Rwork0.18 6229 -
obs--97.2 %

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