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- PDB-6jra: ZHD/W183F complex with hydrolyzed aZOL -

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Basic information

Entry
Database: PDB / ID: 6jra
TitleZHD/W183F complex with hydrolyzed aZOL
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: 1.8 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,9919
Polymers61,9602
Non-polymers1,0317
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-18 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.514, 89.796, 112.752
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: 30979.938 Da / Num. of mol.: 2 / Mutation: W183F
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / 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.: 415 / 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: 3.23 Å3/Da / Density % sol: 61.92 %
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: 1.8→40 Å / Num. obs: 70759 / % possible obs: 99.6 % / Redundancy: 13.3 % / CC1/2: 0.981 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Net I/σ(I): 32.9
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 3449 / CC1/2: 0.929 / Rpim(I) all: 0.166 / Rrim(I) all: 0.593

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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: 1.8→35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.559 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16644 3664 5.2 %RANDOM
Rwork0.14388 ---
obs0.14503 67020 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å20 Å2
2--0.54 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 68 415 4587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134385
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173994
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.6555997
X-RAY DIFFRACTIONr_angle_other_deg1.6191.5839294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1522.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31415679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.811522
X-RAY DIFFRACTIONr_chiral_restr0.1050.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024951
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02889
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_it1.8051.8822206
X-RAY DIFFRACTIONr_mcbond_other1.7991.882205
X-RAY DIFFRACTIONr_mcangle_it2.3562.8132775
X-RAY DIFFRACTIONr_mcangle_other2.3562.8142776
X-RAY DIFFRACTIONr_scbond_it3.5412.2662179
X-RAY DIFFRACTIONr_scbond_other3.5412.2672180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1983.2433223
X-RAY DIFFRACTIONr_long_range_B_refined5.81724.0355114
X-RAY DIFFRACTIONr_long_range_B_other5.75423.7645058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 282 -
Rwork0.189 4801 -
obs--98.81 %

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