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- EMDB-56813: 15-subunit assembly of cyanide dihydratase from Stutzerimonas stu... -

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Basic information

Entry
Database: EMDB / ID: EMD-56813
Title15-subunit assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
Map data
Sample
  • Complex: 14 subunit helical assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
    • Protein or peptide: Cyanide degrading enzyme
KeywordsCyanide degrading enzyme / multimeric assembly / 15mer / HYDROLASE
Function / homology:
Function and homology information
Biological speciesStutzerimonas stutzeri ATCC 14405 = CCUG 16156 (bacteria) / Stutzerimonas (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsDlamini LS / Harrison P / Quigley A / Sewell BT
Funding support South Africa, European Union, 2 items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
iNEXT-DiscoveryEuropean Union
CitationJournal: To Be Published
Title: Cyanide dihydratase from Pseudomonas stutzeri AK1
Authors: Dlamini LS / Sewell BT
History
DepositionFeb 18, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56813.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.85 Å		0.83 Å/pix.
x 350 pix.
= 290.85 Å		0.83 Å/pix.
x 350 pix.
= 290.85 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.292
Minimum - Maximum-0.8965077 - 1.2502906
Average (Standard dev.)0.0011829357 (±0.052202612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.84998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56813_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56813_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 14 subunit helical assembly of cyanide dihydratase from Stutzerim...

EntireName: 14 subunit helical assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
Components
  • Complex: 14 subunit helical assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
    • Protein or peptide: Cyanide degrading enzyme

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Supramolecule #1: 14 subunit helical assembly of cyanide dihydratase from Stutzerim...

SupramoleculeName: 14 subunit helical assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Stutzerimonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Molecular weightTheoretical: 666 kDa/nm

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Macromolecule #1: Cyanide degrading enzyme

MacromoleculeName: Cyanide degrading enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Stutzerimonas (bacteria)
Molecular weightTheoretical: 35.401867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHYPKFKAA AVQAAPVYLN LDATVEKSVK LIEEAASNGA KLVAFPEAFI PGYPWFAFLG HPEYTRRFYH TLYLNAVEIP SEAVQKISA AARKNKIYVC ISCSEKDGGS LYLAQLWFNP EGDLIGKHRK MRVSVAERLC WGDGNGSMMP VFETEIGNLG G LMCWEHNV ...String:
MAHYPKFKAA AVQAAPVYLN LDATVEKSVK LIEEAASNGA KLVAFPEAFI PGYPWFAFLG HPEYTRRFYH TLYLNAVEIP SEAVQKISA AARKNKIYVC ISCSEKDGGS LYLAQLWFNP EGDLIGKHRK MRVSVAERLC WGDGNGSMMP VFETEIGNLG G LMCWEHNV PLDIAAMNSQ NEQVHVAAWP GFFDDETASS HYAICNQAFV LMTSSIYSEE MKDMLCETQE ERDYFNTFKS GH TRIYGPD GEPISDLVPA ETEGIAYAEI DIEKIIDFKY YIDPVGHYSN QSLSMNFNQS PNPVVRKIGE RDSTVFTY

UniProtKB: UNIPROTKB: Q52445

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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

Concentration0.5 mg/mL
BufferpH: 5.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1
#0 - Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
#0 - Average electron dose: 1.2 e/Å2 / #1 - Image recording ID: 2
#1 - Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
#1 - Average electron dose: 1.2 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #0 - Details: ab initio model / #1 - Type of model: OTHER / #1 - Details: ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 857344
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 5

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Image processing #2

Image processing ID2
Image recording ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #0 - Details: ab initio / #1 - Type of model: NONE / #1 - Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 857344
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: AutoBuild on PHENIX as used o create the initial model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-28to:
15-subunit assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)

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Atomic model buiding 2

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: Further fitting and refinement was done using ISOLDE
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-28to:
15-subunit assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)

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