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- EMDB-35452: Cryo-EM structure of ochratoxin A-detoxifying amidohydrolase ADH3 -

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Basic information

Entry
Database: EMDB / ID: EMD-35452
TitleCryo-EM structure of ochratoxin A-detoxifying amidohydrolase ADH3
Map data
Sample
  • Complex: ADH3
    • Protein or peptide: Amidohydrolase family protein
  • Ligand: ZINC ION
Keywordsamidohydrolase / octamer / ochratoxin A degradtion / cryo-EM structure / HYDROLASE
Function / homologyhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Amidohydrolase family protein
Function and homology information
Biological speciesStenotrophomonas acidaminiphila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsDai LH / Niu D / Huang J-W / Li X / Shen PP / Li H / Hu YM / Yang Y / Chen C-C / Guo R-T
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: J Hazard Mater / Year: 2023
Title: Cryo-EM structure and rational engineering of a superefficient ochratoxin A-detoxifying amidohydrolase.
Authors: Dai L / Niu D / Huang JW / Li X / Shen P / Li H / Xie Z / Min J / Hu Y / Yang Y / Guo RT / Chen CC
History
DepositionFeb 23, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_35452.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.99859303 - 1.7493086
Average (Standard dev.)0.0011987791 (±0.048941795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ADH3

EntireName: ADH3
Components
  • Complex: ADH3
    • Protein or peptide: Amidohydrolase family protein
  • Ligand: ZINC ION

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Supramolecule #1: ADH3

SupramoleculeName: ADH3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Stenotrophomonas acidaminiphila (bacteria)

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Macromolecule #1: Amidohydrolase family protein

MacromoleculeName: Amidohydrolase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Stenotrophomonas acidaminiphila (bacteria)
Molecular weightTheoretical: 45.717617 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPIRRRFASL LLLACAPAWA EPVAVQCGRL FDARSGQLKG PHTLLVADGR IRQVLPGTGA DAAGARVVDL GDKVCLPGWT DLHVHLGSQ SSPQSYSEDF RLDPVDHAFR AVGYAEKTLM AGFTSVRDLG GEVSPHLRDA INQGLVRGPR IFAAGKSIAT T GGHADPTN ...String:
MPIRRRFASL LLLACAPAWA EPVAVQCGRL FDARSGQLKG PHTLLVADGR IRQVLPGTGA DAAGARVVDL GDKVCLPGWT DLHVHLGSQ SSPQSYSEDF RLDPVDHAFR AVGYAEKTLM AGFTSVRDLG GEVSPHLRDA INQGLVRGPR IFAAGKSIAT T GGHADPTN GWNERLAHLV GAPGPAEGVV NSVDEARQAV RQRYKEGSDL I(KCX)ITATGGVL SYARSGDAPQ FTVDEIKA V VDTARDYGFR VAAHAHGTEG MKRAVQAGVT SIEHGTYMDD EVMRLMKQHG TWYVPTFYAG RFVTEKAAID GYFPEVVRP KAARIGALIS QTAAKAYRNG VRIAFGTDQG VGPHGDNARE FVYMVEAGIP AAYALQAATV HAAQVLGVDD QGVLEPGKRA DVIALAGNP LEDINAVLDV RFVMKDGVIY KQ

UniProtKB: Amidohydrolase family protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 16 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCL,pH 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2qs8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141155
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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