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- PDB-6jr5: ZHD/H242A complex with bZOL -

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Basic information

Entry
Database: PDB / ID: 6jr5
TitleZHD/H242A complex with bZOL
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-ZHB / Zearalenone lactonase
Function and homology information
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,7296
Polymers61,9042
Non-polymers8254
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.610, 91.680, 113.640
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-ZHB / (3S,7S,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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.14 Å3/Da / Density % sol: 60.82 %
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: 0.97916 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.08→113.64 Å / Num. obs: 47254 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.063 / Net I/σ(I): 12.2
Reflection shellResolution: 2.08→2.13 Å / Rmerge(I) obs: 0.627 / Num. unique obs: 3470 / CC1/2: 0.866 / Rpim(I) all: 0.37

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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: 2.08→35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.485 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23508 2354 5 %RANDOM
Rwork0.18908 ---
obs0.1913 44837 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å2-0 Å2-0 Å2
2---0.42 Å20 Å2
3---2.66 Å2
Refinement stepCycle: 1 / Resolution: 2.08→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 58 215 4359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173931
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6545974
X-RAY DIFFRACTIONr_angle_other_deg1.4371.5829153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9385556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82823.168202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82715664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2721520
X-RAY DIFFRACTIONr_chiral_restr0.0770.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02874
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_it2.7283.5262197
X-RAY DIFFRACTIONr_mcbond_other2.7163.5252196
X-RAY DIFFRACTIONr_mcangle_it3.7565.292762
X-RAY DIFFRACTIONr_mcangle_other3.7585.2912763
X-RAY DIFFRACTIONr_scbond_it3.6313.9362163
X-RAY DIFFRACTIONr_scbond_other3.633.9372164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3215.743213
X-RAY DIFFRACTIONr_long_range_B_refined6.73342.9594934
X-RAY DIFFRACTIONr_long_range_B_other6.72542.9034919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.078→2.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 197 -
Rwork0.291 3260 -
obs--99.54 %

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