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- EMDB-70376: The structure of a Bacterial Cyanide Dihydratase from Bacillus sa... -

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Basic information

Entry
Database: EMDB / ID: EMD-70376
TitleThe structure of a Bacterial Cyanide Dihydratase from Bacillus safensis PER-URP-08
Map dataC1 reconstruction of the Cyanide dihydratase (CynD) from Bacillus safensis PER-URP-08
Sample
  • Complex: Quaternary left-handed helix of cyanide dihydratase dimers
    • Protein or peptide: Cyanide dihydratase
KeywordsCynD / nitrilase / biorremediation / oligomer / HYDROLASE
Function / homology
Function and homology information


nitrilase / nitrilase activity / detoxification of nitrogen compound / nitrile hydratase activity
Similarity search - Function
Nitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesBacillus safensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsJusto Arevalo S / Valle-Riestra F V / Balan A / Chuck CS
Funding support Brazil, 2 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/00943-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
CitationJournal: Structure / Year: 2026
Title: The single-particle cryo-EM structures of a bacterial cyanide dihydratase and a fungal cyanide hydratase.
Authors: Santiago Justo Arevalo / Valeria Valle-Riestra Felice / Mikaela Barahona Acuña / Katia Ordinola Flores / Mauro Quiñones Aguilar / Andrea Balan / Chuck Shaker Farah /
Abstract: Cyanide is widely used in industries due to its affinity for metals, a property that also underlies its toxicity. Industries, therefore, must reduce cyanide concentration before the final disposal of ...Cyanide is widely used in industries due to its affinity for metals, a property that also underlies its toxicity. Industries, therefore, must reduce cyanide concentration before the final disposal of wastewater. Physical, chemical, and biological methods have been developed for this; however, knowledge about the structure of enzymes involved in cyanide degradation remains limited. Structural characterization of these proteins could facilitate the development of enzymes with enhanced bioremediation potential. Here, we present the single-particle cryo-electron microscopy structures of a cyanide dihydratase from Bacillus safensis and a cyanide hydratase from Gloeocercospora sorghi at 2.2 Å and 2.0 Å resolution, respectively. We provide a comprehensive description and comparative analysis alongside all previously determined nitrilase structures. Importantly, our full-length structures reveal new features in the C-terminal as well as specific intermolecular interactions between protomer interfaces and within the helix lumen. Finally, our findings offer insights into the reaction mechanisms of these two enzymes.
History
DepositionApr 27, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70376.png

Downloads & links

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Map

FileDownload / File: emd_70376.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1 reconstruction of the Cyanide dihydratase (CynD) from Bacillus safensis PER-URP-08
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 550 pix.
= 400.95 Å		0.73 Å/pix.
x 550 pix.
= 400.95 Å		0.73 Å/pix.
x 550 pix.
= 400.95 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.9101948 - 3.3331
Average (Standard dev.)-0.0014833694 (±0.08752822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 400.94998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70376_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map with helical axis aligned to the Z-axis....

Fileemd_70376_additional_1.map
AnnotationMap with helical axis aligned to the Z-axis. This map could have slightly less resolution than the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of C1 reconstruction of the...

Fileemd_70376_half_map_1.map
AnnotationHalf map A of C1 reconstruction of the Cyanide dihydratase (CynD) from Bacillus safensis PER-URP-08
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of C1 reconstruction of the...

Fileemd_70376_half_map_2.map
AnnotationHalf map B of C1 reconstruction of the Cyanide dihydratase (CynD) from Bacillus safensis PER-URP-08
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Quaternary left-handed helix of cyanide dihydratase dimers

EntireName: Quaternary left-handed helix of cyanide dihydratase dimers
Components
  • Complex: Quaternary left-handed helix of cyanide dihydratase dimers
    • Protein or peptide: Cyanide dihydratase

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Supramolecule #1: Quaternary left-handed helix of cyanide dihydratase dimers

SupramoleculeName: Quaternary left-handed helix of cyanide dihydratase dimers
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: wild type CynD from Bacillus safensis PER-URP-08
Source (natural)Organism: Bacillus safensis (bacteria) / Strain: PER-URP-08
Molecular weightTheoretical: 677.232 KDa

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Macromolecule #1: Cyanide dihydratase

MacromoleculeName: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Details: Monomer of CynD / Number of copies: 18 / Enantiomer: LEVO / EC number: nitrilase
Source (natural)Organism: Bacillus safensis (bacteria) / Strain: PER-URP-08
Molecular weightTheoretical: 37.526223 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTSIYPKFRA AAVQAAPVYL NLEATVEKSC ELIDEAASNG AKLVAFPEAF LPGYPWFAFI GHPEYTRKFY HELYKNAVEI PSLAIQKIS EAAKRNETYV CISCSEKDGG SLYLAQLWFN PNGDLIGKHR KMRASVAERL IWGDGSGSMM PVFQTDIGNL G GLMCWEHQ ...String:
MTSIYPKFRA AAVQAAPVYL NLEATVEKSC ELIDEAASNG AKLVAFPEAF LPGYPWFAFI GHPEYTRKFY HELYKNAVEI PSLAIQKIS EAAKRNETYV CISCSEKDGG SLYLAQLWFN PNGDLIGKHR KMRASVAERL IWGDGSGSMM PVFQTDIGNL G GLMCWEHQ VPLDLMAMNA QNEQVHVASW PGYFDDEISS RYYAIATQTF VLMTSSIYTE EMKEMICLTQ EQRDYFETFK SG HTCIYGP DGEPISDMVP AETEGIAYAE IDVERVIDYK YYIDPAGHYS NQSLSMNFNQ QPTPVVKQLY HQKNEVFTYE DIQ YQHGIL EEKV

UniProtKB: Nitrilase

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 3993 / Average exposure time: 4.39 sec. / Average electron dose: 55.59 e/Å2
Details: Number of processing frames fractions collected were 30
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: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 822794
CTF correctionSoftware - Name: cisTEM (ver. 1.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Initial model constructed by cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 361080
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 90270 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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