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- EMDB-66036: Cryo-EM structure of DONepi, a deoxynivalenol 3-epimerase from No... -

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Basic information

Entry
Database: EMDB / ID: EMD-66036
TitleCryo-EM structure of DONepi, a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5
Map data
Sample
  • Complex: a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5
    • Protein or peptide: DON 3-epimerase chain D
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsDON degradation / DON 3-epimerase / aldo-keto reductase / octamer / OXIDOREDUCTASE
Biological speciesNocardioides sp. S5-5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHe WJ / Wu AB / Xiong RY
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32025030 China
CitationJournal: To Be Published
Title: Cryo-EM structure of DONepi, a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5
Authors: He WJ / Wu AB / Xiong RY
History
DepositionSep 1, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66036.png

Downloads & links

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Map

FileDownload / File: emd_66036.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 247.2 Å		0.82 Å/pix.
x 300 pix.
= 247.2 Å		0.82 Å/pix.
x 300 pix.
= 247.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.172
Minimum - Maximum-0.35612926 - 0.8428734
Average (Standard dev.)0.0032282374 (±0.036659785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_66036_half_map_1.map
Annotationhalf_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_66036_half_map_2.map
Annotationhalf_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5

EntireName: a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5
Components
  • Complex: a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5
    • Protein or peptide: DON 3-epimerase chain D
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5

SupramoleculeName: a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nocardioides sp. S5-5 (bacteria)

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Macromolecule #1: DON 3-epimerase chain D

MacromoleculeName: DON 3-epimerase chain D / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Nocardioides sp. S5-5 (bacteria)
Molecular weightTheoretical: 38.144559 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMDYRVLGRT GVKVSPLTLG TMNFGSYGKV SAPAGAELID RALEAGINVI DTADVYSATE SESIIGAALA VSGRREDVVL ASKFNRPLD KDPNHRGNSR RWIRRAVEDS LRRLQTDHLD IYYAHRPDED TELEETVDTL VDLVREGKVL YYGTSTFPTS Q IVEAQWLG ...String:
MMDYRVLGRT GVKVSPLTLG TMNFGSYGKV SAPAGAELID RALEAGINVI DTADVYSATE SESIIGAALA VSGRREDVVL ASKFNRPLD KDPNHRGNSR RWIRRAVEDS LRRLQTDHLD IYYAHRPDED TELEETVDTL VDLVREGKVL YYGTSTFPTS Q IVEAQWLG RSRGVRPTVE QPPYSILVRH GERELLPTAS AHGLGTFAWS PLAGGWLSGH YRQSDNGDQW TRWNNALRHD PE LDVNKRK SAAVAQLEDL ANAAGLSLVQ LAIGFVLEHP AVTSAIIGPR TVEQLDAYLS AADTVLDSDT LDAIDRIVAP GET LSPGDI GDDPLPIRQP RLRRRHHRGE

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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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

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 229168
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9wk1:
Cryo-EM structure of DONepi, a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5

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