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- PDB-5c7y: ZHD-Intermediate complex after ZHD crystal soaking in ZEN for 9min -

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Basic information

Entry
Database: PDB / ID: 5c7y
TitleZHD-Intermediate complex after ZHD crystal soaking in ZEN for 9min
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
FORMIC ACID / : / Chem-ZFR / Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 ChinaNo. 2009CB918602 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)63,11512
Polymers62,0382
Non-polymers1,07710
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-18 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.690, 89.670, 113.200
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, 413 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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-FMT / 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: isolated from a natural source / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 1.75→50 Å / Num. obs: 76939 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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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: 1.75→47.863 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 3839 4.99 %Random
Rwork0.153 ---
obs0.1544 76860 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 71 403 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074586
X-RAY DIFFRACTIONf_angle_d1.0616297
X-RAY DIFFRACTIONf_dihedral_angle_d12.6731679
X-RAY DIFFRACTIONf_chiral_restr0.045696
X-RAY DIFFRACTIONf_plane_restr0.005836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77220.21941330.18122689X-RAY DIFFRACTION100
1.7722-1.79550.2251350.17922711X-RAY DIFFRACTION100
1.7955-1.82010.20291420.18012679X-RAY DIFFRACTION100
1.8201-1.84610.18891340.16092663X-RAY DIFFRACTION100
1.8461-1.87360.19971530.15952716X-RAY DIFFRACTION100
1.8736-1.90290.22281310.15052647X-RAY DIFFRACTION100
1.9029-1.93410.18291530.14812665X-RAY DIFFRACTION100
1.9341-1.96750.17351430.14212698X-RAY DIFFRACTION100
1.9675-2.00320.17181750.13972659X-RAY DIFFRACTION100
2.0032-2.04180.17091310.14352687X-RAY DIFFRACTION100
2.0418-2.08350.17891370.14162724X-RAY DIFFRACTION100
2.0835-2.12880.18091450.14962656X-RAY DIFFRACTION100
2.1288-2.17830.15881450.14052680X-RAY DIFFRACTION100
2.1783-2.23270.16531480.14052693X-RAY DIFFRACTION100
2.2327-2.29310.16751350.14412708X-RAY DIFFRACTION100
2.2931-2.36060.19431430.14852684X-RAY DIFFRACTION100
2.3606-2.43680.18611370.1472693X-RAY DIFFRACTION100
2.4368-2.52390.16651550.14992687X-RAY DIFFRACTION100
2.5239-2.62490.19271300.15512719X-RAY DIFFRACTION99
2.6249-2.74440.19011130.15042732X-RAY DIFFRACTION100
2.7444-2.8890.17811530.14412703X-RAY DIFFRACTION99
2.889-3.070.17291480.1532704X-RAY DIFFRACTION99
3.07-3.3070.15741460.14592721X-RAY DIFFRACTION99
3.307-3.63970.18531450.14432701X-RAY DIFFRACTION98
3.6397-4.16610.16271570.14242689X-RAY DIFFRACTION97
4.1661-5.24780.20451090.15982826X-RAY DIFFRACTION100
5.2478-47.88070.19721630.19652887X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.3745 Å / Origin y: 16.0038 Å / Origin z: -5.8549 Å
111213212223313233
T0.0662 Å20.0004 Å2-0.002 Å2-0.096 Å2-0.0225 Å2--0.0998 Å2
L0.1781 °20.0496 °2-0.0793 °2-0.5908 °2-0.433 °2--0.7104 °2
S0.0161 Å °0.01 Å °0.0007 Å °-0.0026 Å °0.0047 Å °0.022 Å °-0.0109 Å °0.0284 Å °-0.0188 Å °
Refinement TLS groupSelection details: ALL

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