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- PDB-6jr2: ZHD/H242A complex with aZOL -

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Basic information

Entry
Database: PDB / ID: 6jr2
TitleZHD/H242A complex with 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-36J / : / 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 2, 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)63,26713
Polymers61,9042
Non-polymers1,36411
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-20 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.905, 90.427, 112.355
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: 30951.902 Da / Num. of mol.: 2 / Mutation: H242A
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-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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / 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.: 400 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
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: 91938 / % possible obs: 99.2 % / Redundancy: 13.3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Net I/σ(I): 42.5
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 4528 / CC1/2: 0.929 / Rpim(I) all: 0.173 / Rrim(I) all: 0.639

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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: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.05 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15778 4697 5.1 %RANDOM
Rwork0.14046 ---
obs0.14137 87168 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.19 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 90 400 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134512
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174061
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.6386184
X-RAY DIFFRACTIONr_angle_other_deg1.6581.5579471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24223.14207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01215686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6531521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025140
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02903
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_it1.8421.8062255
X-RAY DIFFRACTIONr_mcbond_other1.8411.8042254
X-RAY DIFFRACTIONr_mcangle_it2.4352.7022852
X-RAY DIFFRACTIONr_mcangle_other2.4352.7042853
X-RAY DIFFRACTIONr_scbond_it3.3932.1542257
X-RAY DIFFRACTIONr_scbond_other3.3932.1552258
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8773.0873333
X-RAY DIFFRACTIONr_long_range_B_refined5.8623.2425291
X-RAY DIFFRACTIONr_long_range_B_other5.8623.2545292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.648→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 336 -
Rwork0.179 6289 -
obs--97.96 %

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