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- PDB-6jrd: ZHD complex with hydrolyzed beta-ZOL -

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Basic information

Entry
Database: PDB / ID: 6jrd
TitleZHD complex with hydrolyzed beta-ZOL
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / LACTONASE / ALPHA-BETA FOLD / ZEARALENONE DEGRADE
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
Similarity search - Domain/homology
Chem-C1U / : / Zearalenone hydrolase
Similarity search - Component
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,53014
Polymers62,0382
Non-polymers1,49212
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-20 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.536, 89.969, 112.728
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) / Gene: zhd101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NKB0
#2: Chemical ChemComp-C1U / 2-[(~{E},6~{S},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.: 8 / 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.: 473 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRAIN OF CLONOSTACHYS ROSEA IS DIFFERENT FROM UNP Q8NKB0.

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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: 59.62 %
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: 91529 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Net I/σ(I): 36
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.54 / Num. unique obs: 4495 / CC1/2: 0.953 / Rpim(I) all: 0.14 / Rrim(I) all: 0.523 / % possible all: 100

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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: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.105 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.161 4695 5.1 %RANDOM
Rwork0.138 ---
obs0.139 86749 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.66 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 98 473 4681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134551
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174083
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.6536238
X-RAY DIFFRACTIONr_angle_other_deg1.6611.5829530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4823.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14415696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7441520
X-RAY DIFFRACTIONr_chiral_restr0.1140.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025194
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02912
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_it1.8271.8472278
X-RAY DIFFRACTIONr_mcbond_other1.8271.8452277
X-RAY DIFFRACTIONr_mcangle_it2.4342.7662886
X-RAY DIFFRACTIONr_mcangle_other2.4342.7682887
X-RAY DIFFRACTIONr_scbond_it3.4282.2352273
X-RAY DIFFRACTIONr_scbond_other3.4272.2362274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8643.1983353
X-RAY DIFFRACTIONr_long_range_B_refined5.73823.945329
X-RAY DIFFRACTIONr_long_range_B_other5.67123.6595272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 339 -
Rwork0.181 6271 -
obs--98.64 %

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