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- PDB-5c81: ZHD-Intermediate complex after ZHD crystal soaking in ZEN for 12min -

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Basic information

Entry
Database: PDB / ID: 5c81
TitleZHD-Intermediate complex after ZHD crystal soaking in ZEN for 12min
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-ZFR / Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
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 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)62,8398
Polymers62,0382
Non-polymers8016
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.530, 90.080, 112.920
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, 505 molecules

#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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / 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.: 499 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 70972 / % possible obs: 99.8 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 6.7 / % possible all: 99.7

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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: 1.8→47.84 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 3471 4.9 %Random selection
Rwork0.1479 ---
obs0.1493 70897 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 53 499 4646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074448
X-RAY DIFFRACTIONf_angle_d1.0586107
X-RAY DIFFRACTIONf_dihedral_angle_d11.9451613
X-RAY DIFFRACTIONf_chiral_restr0.045688
X-RAY DIFFRACTIONf_plane_restr0.005801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.82470.1961480.17952647X-RAY DIFFRACTION100
1.8247-1.85080.17071300.15912673X-RAY DIFFRACTION100
1.8508-1.87840.16821410.14822652X-RAY DIFFRACTION100
1.8784-1.90780.17471300.14272668X-RAY DIFFRACTION100
1.9078-1.9390.19281370.14352641X-RAY DIFFRACTION100
1.939-1.97250.24191400.1432672X-RAY DIFFRACTION100
1.9725-2.00840.19351310.14412708X-RAY DIFFRACTION100
2.0084-2.0470.17561460.15022652X-RAY DIFFRACTION100
2.047-2.08880.18331380.14532663X-RAY DIFFRACTION100
2.0888-2.13420.1691390.14532673X-RAY DIFFRACTION100
2.1342-2.18380.15961280.13892675X-RAY DIFFRACTION100
2.1838-2.23840.16111370.13912676X-RAY DIFFRACTION100
2.2384-2.2990.17251540.14292679X-RAY DIFFRACTION100
2.299-2.36660.1871500.14892658X-RAY DIFFRACTION100
2.3666-2.4430.17691460.14762689X-RAY DIFFRACTION100
2.443-2.53030.18851290.14722691X-RAY DIFFRACTION100
2.5303-2.63160.19881470.15192689X-RAY DIFFRACTION100
2.6316-2.75140.19771240.15132709X-RAY DIFFRACTION100
2.7514-2.89640.18061470.15262695X-RAY DIFFRACTION100
2.8964-3.07780.1811470.15872706X-RAY DIFFRACTION100
3.0778-3.31540.16361230.15082737X-RAY DIFFRACTION100
3.3154-3.6490.14631320.14722720X-RAY DIFFRACTION100
3.649-4.17670.15441290.13192772X-RAY DIFFRACTION100
4.1767-5.26120.16011300.13722784X-RAY DIFFRACTION100
5.2612-47.85660.19161680.17092897X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.3287 Å / Origin y: 16.3747 Å / Origin z: -5.7321 Å
111213212223313233
T0.0833 Å20.0035 Å2-0.006 Å2-0.1158 Å2-0.0231 Å2--0.12 Å2
L0.2325 °2-0.0069 °2-0.0336 °2-0.6786 °2-0.5041 °2--0.7948 °2
S0.0112 Å °0.0124 Å °-0.0037 Å °-0.0252 Å °0.008 Å °0.0339 Å °0.0139 Å °0.0359 Å °-0.0172 Å °
Refinement TLS groupSelection details: ALL

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