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- PDB-9m5g: Crystal structure of a thermostable zearalenone-degrading lactona... -

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Basic information

Entry
Database: PDB / ID: 9m5g
TitleCrystal structure of a thermostable zearalenone-degrading lactonase mutant - S102A with ligand zearalenone
ComponentsAB hydrolase-1 domain-containing protein
KeywordsHYDROLASE / Complex
Function / homologyChem-ZER / :
Function and homology information
Biological speciesMonosporascus sp. GIB2 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 thermostable zearalenone-degrading lactonase mutant - S102A with ligand zearalenone
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)30,1022
Polymers29,7841
Non-polymers3181
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)60,2044
Polymers59,5682
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.661, 73.661, 95.454
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

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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
Details: mutant S102A / Source: (gene. exp.) Monosporascus sp. GIB2 (fungus) / Gene: DL765_008938 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q4TP46
#2: Chemical ChemComp-ZER / (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione / Zearalenone


Mass: 318.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Magnesium chloride, 0.05M 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 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→24.04 Å / Num. obs: 17936 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.51 / Num. unique obs: 2180 / CC1/2: 0.858 / Rpim(I) all: 0.265 / Rrim(I) all: 0.576

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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: 2.1→22.53 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 998 5.56 %
Rwork0.1937 --
obs0.1964 17936 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→22.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 31 185 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072174
X-RAY DIFFRACTIONf_angle_d0.8912961
X-RAY DIFFRACTIONf_dihedral_angle_d16.704794
X-RAY DIFFRACTIONf_chiral_restr0.052322
X-RAY DIFFRACTIONf_plane_restr0.009381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.28231170.24562381X-RAY DIFFRACTION99
2.21-2.350.29521520.22932377X-RAY DIFFRACTION100
2.35-2.530.27351710.23032357X-RAY DIFFRACTION100
2.53-2.780.28411340.21932409X-RAY DIFFRACTION100
2.78-3.190.27461400.2082426X-RAY DIFFRACTION100
3.19-4.010.20581540.17632431X-RAY DIFFRACTION100
4.01-22.530.20741300.16272557X-RAY DIFFRACTION100

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