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- PDB-5c8z: ZHD-ZGR complex after ZHD crystal soaking in ZEN for 30min -

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Basic information

Entry
Database: PDB / ID: 5c8z
TitleZHD-ZGR complex after ZHD crystal soaking in ZEN for 30min
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / lactonase / alpha-beta fold / zearalenone degrade intermediate
Function / homology
Function and homology information


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
FORMIC ACID / : / Chem-ZGR / Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The structure of a complex of the lactonohydrolase zearalenone hydrolase with the hydrolysis product of zearalenone at 1.60 angstrom resolution.
Authors: Qi, Q. / Yang, W.J. / Zhou, H.J. / Ming, D.M. / Sun, K.L. / Xu, T.Y. / Hu, X.J. / Lv, H.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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)63,29513
Polymers62,0382
Non-polymers1,25711
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-17 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.900, 89.590, 113.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 335 molecules

#2: Chemical ChemComp-ZGR / 2,4-dihydroxy-6-[(1E,10S)-10-hydroxy-6-oxoundec-1-en-1-yl]benzoic acid


Mass: 336.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C18H24O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.6→50 Å / Num. obs: 101351 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZL

3wzl


Resolution: 1.6→48.028 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 5060 5 %Random selection
Rwork0.1535 ---
obs0.1542 101261 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→48.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 83 324 4483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064559
X-RAY DIFFRACTIONf_angle_d1.1176262
X-RAY DIFFRACTIONf_dihedral_angle_d12.821659
X-RAY DIFFRACTIONf_chiral_restr0.047693
X-RAY DIFFRACTIONf_plane_restr0.006827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.19811750.17263139X-RAY DIFFRACTION100
1.6182-1.63720.17751710.16643148X-RAY DIFFRACTION100
1.6372-1.65720.18341710.16463191X-RAY DIFFRACTION100
1.6572-1.67820.20881580.16223181X-RAY DIFFRACTION100
1.6782-1.70030.18891630.15993210X-RAY DIFFRACTION100
1.7003-1.72360.19581620.15863172X-RAY DIFFRACTION100
1.7236-1.74820.20051510.15853202X-RAY DIFFRACTION100
1.7482-1.77430.18411510.15023182X-RAY DIFFRACTION100
1.7743-1.8020.16781740.14653165X-RAY DIFFRACTION100
1.802-1.83150.16011620.14393223X-RAY DIFFRACTION100
1.8315-1.86310.15081490.13623182X-RAY DIFFRACTION100
1.8631-1.8970.14421640.13723202X-RAY DIFFRACTION100
1.897-1.93350.17241780.13283144X-RAY DIFFRACTION100
1.9335-1.9730.16221670.13133208X-RAY DIFFRACTION100
1.973-2.01590.13221620.13733190X-RAY DIFFRACTION100
2.0159-2.06280.16041770.14193204X-RAY DIFFRACTION100
2.0628-2.11430.14431680.14193171X-RAY DIFFRACTION100
2.1143-2.17150.15851720.14693193X-RAY DIFFRACTION100
2.1715-2.23540.14661770.14483214X-RAY DIFFRACTION100
2.2354-2.30760.15911710.14343187X-RAY DIFFRACTION100
2.3076-2.390.16481880.15073214X-RAY DIFFRACTION100
2.39-2.48570.15651580.153213X-RAY DIFFRACTION100
2.4857-2.59880.16351680.15783218X-RAY DIFFRACTION100
2.5988-2.73580.16841690.15483233X-RAY DIFFRACTION100
2.7358-2.90720.14981840.14433222X-RAY DIFFRACTION100
2.9072-3.13170.15091600.14533244X-RAY DIFFRACTION100
3.1317-3.44670.15571820.14633243X-RAY DIFFRACTION100
3.4467-3.94530.15991760.14513271X-RAY DIFFRACTION100
3.9453-4.96980.1981630.16453312X-RAY DIFFRACTION100
4.9698-48.05010.20581890.20813323X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 18.465 Å / Origin y: 15.9828 Å / Origin z: -5.595 Å
111213212223313233
T0.0886 Å2-0.0044 Å2-0.0002 Å2-0.1125 Å2-0.0173 Å2--0.1173 Å2
L0.2091 °20.0442 °2-0.0899 °2-0.4851 °2-0.3232 °2--0.6038 °2
S0.0204 Å °0.006 Å °-0.0001 Å °0.0071 Å °0.0051 Å °0.008 Å °-0.0281 Å °0.0142 Å °-0.0247 Å °
Refinement TLS groupSelection details: ALL

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