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- PDB-9m5f: zearalenone degrading enzyme with a-zearalenol -

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Basic information

Entry
Database: PDB / ID: 9m5f
Titlezearalenone degrading enzyme with a-zearalenol
ComponentsAB hydrolase-1 domain-containing protein
KeywordsHYDROLASE / Complex
Function / homologyChem-36J / :
Function and homology information
Biological speciesMonosporascus sp. GIB2 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOuyang, B. / Xu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22408125 China
CitationJournal: To Be Published
Title: Crystal structure of a novel thermostable zearalenone degrading enzyme with a-zearalenol
Authors: Ouyang, B. / Xu, W.
History
DepositionMar 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AB hydrolase-1 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1042
Polymers29,7841
Non-polymers3201
Water1,40578
1
A: AB hydrolase-1 domain-containing protein
hetero molecules

A: AB hydrolase-1 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2084
Polymers59,5682
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.790, 73.790, 95.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AB hydrolase-1 domain-containing protein / zearalenone degrading enzyme


Mass: 29783.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosporascus sp. GIB2 (fungus) / Gene: DL765_008938 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q4TP46
#2: Chemical ChemComp-36J / (3S,7R,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one


Mass: 320.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Magnesium chloride, 0.05 M Tris-HCl pH 8.5, 30% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.24→63.96 Å / Num. obs: 10730 / % possible obs: 98.8 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.03 / Rrim(I) all: 0.131 / Χ2: 0.97 / Net I/σ(I): 19.7 / Num. measured all: 274187
Reflection shellResolution: 2.24→2.3 Å / % possible obs: 88.1 % / Redundancy: 14.6 % / Rmerge(I) obs: 1.983 / Num. measured all: 13993 / Num. unique obs: 961 / CC1/2: 0.643 / Rpim(I) all: 0.521 / Rrim(I) all: 2.054 / Χ2: 0.94 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L7M

6l7m


Resolution: 2.35→38.2 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 597 5.56 %
Rwork0.1878 --
obs0.1905 10730 82.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 23 78 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082175
X-RAY DIFFRACTIONf_angle_d0.9372964
X-RAY DIFFRACTIONf_dihedral_angle_d17.683795
X-RAY DIFFRACTIONf_chiral_restr0.047323
X-RAY DIFFRACTIONf_plane_restr0.01381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.580.2735580.24341096X-RAY DIFFRACTION36
2.58-2.950.28561960.21062798X-RAY DIFFRACTION93
2.96-3.720.22911730.21033055X-RAY DIFFRACTION100
3.73-38.20.21521700.16053184X-RAY DIFFRACTION99

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