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- EMDB-17409: Cyanide dihydratase from Bacillus pumilus C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-17409
TitleCyanide dihydratase from Bacillus pumilus C1
Map dataCyanide dihydratase from Bacillus pumilus C1
Sample
  • Complex: Wildtype cyanide dihydratase from Bacillus pumilus C1
    • Protein or peptide: Cyanide dihydratase
KeywordsCyanide degrading enzyme / HYDROLASE
Function / homologyNitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / nitrilase activity / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / Cyanide dihydratase
Function and homology information
Biological speciesBacillus pumilus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsMulelu AE / Reitz J / van Rooyen JM / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT
Funding support South Africa, 1 items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
CitationJournal: To Be Published
Title: The Role of Histidine Residues in the Oligomerization of Cyanide Dihydratase from Bacillus pumilus C1
Authors: Mulelu AE / Reitz J / van Rooyen J / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT
History
DepositionMay 22, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17409.png

Downloads & links

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Map

FileDownload / File: emd_17409.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCyanide dihydratase from Bacillus pumilus C1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0119
Minimum - Maximum-0.020919774 - 0.04766187
Average (Standard dev.)0.0003063033 (±0.0022641555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Wildtype cyanide dihydratase from Bacillus pumilus C1

EntireName: Wildtype cyanide dihydratase from Bacillus pumilus C1
Components
  • Complex: Wildtype cyanide dihydratase from Bacillus pumilus C1
    • Protein or peptide: Cyanide dihydratase

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Supramolecule #1: Wildtype cyanide dihydratase from Bacillus pumilus C1

SupramoleculeName: Wildtype cyanide dihydratase from Bacillus pumilus C1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Homo-oligomeric 18mer expressed recombinantly without a purification tag.
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 0.666 kDa/nm

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Macromolecule #1: Cyanide dihydratase

MacromoleculeName: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 35.941418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SIYPKFRAAA VQAAPIYLNL EASVEKSCEL IDEAASNGAK LVAFPEAFLP GYPWFAFIGH PEYTRKFYHE LYKNAVEIPS LAIQKISEA AKRNETYVCI SCSEKDGGSL YLAQLWFNPN GDLIGKHRKM RASVAERLIW GDGSGSMMPV FQTEIGNLGG L MCWEHQVP ...String:
SIYPKFRAAA VQAAPIYLNL EASVEKSCEL IDEAASNGAK LVAFPEAFLP GYPWFAFIGH PEYTRKFYHE LYKNAVEIPS LAIQKISEA AKRNETYVCI SCSEKDGGSL YLAQLWFNPN GDLIGKHRKM RASVAERLIW GDGSGSMMPV FQTEIGNLGG L MCWEHQVP LDLMAMNAQN EQVHVASWPG YFDDEISSRY YAIATQTFVL MTSSIYTEEM KEMICLTQEQ RDYFETFKSG HT CIYGPDG EPISDMVPAE TEGIAYAEID VERVIDYKYY IDPAGHYSNQ SLSMNFNQQP TPVVKHLNHQ KNEVFTYEDI

UniProtKB: Cyanide dihydratase

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 5.4 / Component - Concentration: 50.0 mM / Component - Formula: C6H8O7 / Component - Name: citrate
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -77 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 120943
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8p4i:
Cyanide dihydratase from Bacillus pumilus C1

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