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- PDB-5c8x: ZHD-Intermediate complex after ZHD crystal soaking in ZEN for 20min -

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Basic information

Entry
Database: PDB / ID: 5c8x
TitleZHD-Intermediate complex after ZHD crystal soaking in ZEN for 20min
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / lactonase / alpha-beta fold / zearalenone degrade intermediate
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-ZFR / Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHu, X.-J. / Qi, Q. / Yang, W.-J.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese High-tech Research and Development program2013AA102803B China
Chinese High-tech Research and Development program2014AA021301 China
the 973 Program of the Ministry of Science and Technology of China2009CB918602 China
CitationJournal: To Be Published
Title: A Case Study of Lactonase ZHD
Authors: Ming, D.-M. / Qi, Q. / Yang, W.-J. / Sun, K.-L. / Xu, T.-Y. / Huang, Q. / Hu, X.-J. / Lv, H.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)62,8858
Polymers62,0382
Non-polymers8476
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.580, 89.030, 113.130
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-ZFR / (1E,10S)-1-(3,5-dihydroxyphenyl)-10-hydroxyundec-1-en-6-one


Mass: 292.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 336 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZFR and FMT are used to simulate the intermediate in the crystal structure.
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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.2 M ammonium dibasic phosphate, 200 mM KCl, 100 mM imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70514 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 7.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.8→47.744 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 3510 4.98 %Random selection
Rwork0.1502 ---
obs0.1511 70440 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 56 336 4474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074458
X-RAY DIFFRACTIONf_angle_d1.0726117
X-RAY DIFFRACTIONf_dihedral_angle_d11.4451613
X-RAY DIFFRACTIONf_chiral_restr0.046682
X-RAY DIFFRACTIONf_plane_restr0.006806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82470.20411360.16652661X-RAY DIFFRACTION100
1.8247-1.85070.19241530.14882639X-RAY DIFFRACTION100
1.8507-1.87840.15671380.14322612X-RAY DIFFRACTION100
1.8784-1.90770.19661320.13542680X-RAY DIFFRACTION100
1.9077-1.9390.16641320.13282638X-RAY DIFFRACTION100
1.939-1.97240.16241540.1322664X-RAY DIFFRACTION100
1.9724-2.00830.14881320.13322604X-RAY DIFFRACTION100
2.0083-2.04690.17731510.14162629X-RAY DIFFRACTION100
2.0469-2.08870.18021430.1372666X-RAY DIFFRACTION100
2.0887-2.13410.15541470.13972652X-RAY DIFFRACTION100
2.1341-2.18380.14511490.13562645X-RAY DIFFRACTION100
2.1838-2.23840.17511380.13792648X-RAY DIFFRACTION100
2.2384-2.29890.17871440.14222650X-RAY DIFFRACTION100
2.2989-2.36650.16521200.1462693X-RAY DIFFRACTION100
2.3665-2.44290.18241440.14392638X-RAY DIFFRACTION100
2.4429-2.53020.14941250.14512708X-RAY DIFFRACTION100
2.5302-2.63150.17131330.14952681X-RAY DIFFRACTION100
2.6315-2.75130.16971400.14662668X-RAY DIFFRACTION100
2.7513-2.89630.14321240.1452717X-RAY DIFFRACTION100
2.8963-3.07780.16591520.15092667X-RAY DIFFRACTION100
3.0778-3.31530.15721300.14462707X-RAY DIFFRACTION100
3.3153-3.64890.17691370.14482707X-RAY DIFFRACTION100
3.6489-4.17660.16071490.14952724X-RAY DIFFRACTION100
4.1766-5.2610.1661400.17012769X-RAY DIFFRACTION100
5.261-47.76050.18721670.19082863X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.2952 Å / Origin y: 15.9064 Å / Origin z: 5.588 Å
111213212223313233
T0.0818 Å20.0004 Å2-0.0027 Å2-0.1144 Å20.0211 Å2--0.1161 Å2
L0.2095 °2-0.0346 °2-0.0649 °2-0.6218 °20.4384 °2--0.6862 °2
S0.0139 Å °-0.0153 Å °-0.0121 Å °0.0025 Å °0.0054 Å °-0.0218 Å °-0.0067 Å °-0.0218 Å °-0.02 Å °
Refinement TLS groupSelection details: ALL

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