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- EMDB-16437: Cyanide dihydratase from Bacillus pumilus C1 variant - Q86R,H305K... -

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Basic information

Entry
Database: EMDB / ID: EMD-16437
TitleCyanide dihydratase from Bacillus pumilus C1 variant - Q86R,H305K,H308K,H323K
Map dataMap of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K)
Sample
  • Complex: Active helical nitrilase homo-oligomer of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K)
    • Protein or peptide: Cyanide dihydratase
KeywordsHelical / homo-oligomeric / cyanide dihydratase / 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: 3.15 Å
AuthorsMulelu AE / Reitz J / van Rooyen J / 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
DepositionJan 9, 2023-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16437.png

Downloads & links

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Map

FileDownload / File: emd_16437.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K)
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: 0.0248
Minimum - Maximum-0.073721595 - 0.121908784
Average (Standard dev.)-0.00008425946 (±0.0060234424)
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 : Active helical nitrilase homo-oligomer of cyanide dihydratase fro...

EntireName: Active helical nitrilase homo-oligomer of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K)
Components
  • Complex: Active helical nitrilase homo-oligomer of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K)
    • Protein or peptide: Cyanide dihydratase

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Supramolecule #1: Active helical nitrilase homo-oligomer of cyanide dihydratase fro...

SupramoleculeName: Active helical nitrilase homo-oligomer of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cyanide dihydratase from Bacillus pumilus C1 variant generated by site-directed mutagenesis.
Source (natural)Organism: Bacillus pumilus (bacteria)

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Macromolecule #1: Cyanide dihydratase

MacromoleculeName: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 37.503363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSIYPKFRA AAVQAAPIYL NLEASVEKSC ELIDEAASNG AKLVAFPEAF LPGYPWFAFI GHPEYTRKFY HELYKNAVEI PSLAIRKIS EAAKRNETYV CISCSEKDGG SLYLAQLWFN PNGDLIGKHR KMRASVAERL IWGDGSGSMM PVFQTEIGNL G GLMCWEHQ ...String:
MTSIYPKFRA AAVQAAPIYL NLEASVEKSC ELIDEAASNG AKLVAFPEAF LPGYPWFAFI GHPEYTRKFY HELYKNAVEI PSLAIRKIS EAAKRNETYV CISCSEKDGG SLYLAQLWFN PNGDLIGKHR KMRASVAERL IWGDGSGSMM PVFQTEIGNL G GLMCWEHQ VPLDLMAMNA QNEQVHVASW PGYFDDEISS RYYAIATQTF VLMTSSIYTE EMKEMICLTQ EQRDYFETFK SG HTCIYGP DGEPISDMVP AETEGIAYAE IDVERVIDYK YYIDPAGHYS NQSLSMNFNQ QPTPVVKKLN KQKNEVFTYE DIQ YQKGIL EEKV

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:
ConcentrationFormulaName
0.15 MNaClsodium chloride
0.05 MTristrizma base

Details: 150 mM NaCl, 50 mM Tris-HCl pH 5.4
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 20.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: A 2.5 microlitre sample was applied onto a glow-discharged grid, blotted and plunged without incubation..
DetailsHomogeneous protein sample.

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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: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 92000
Applied symmetry - Helical parameters - Δz: 16.7 Å
Applied symmetry - Helical parameters - Δ&Phi: -77 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 103000
Startup modelType of model: INSILICO MODEL / In silico model: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8c5i:
Cyanide dihydratase from Bacillus pumilus C1 variant - Q86R,H305K,H308K,H323K

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