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- PDB-28to: 15-subunit assembly of cyanide dihydratase from Stutzerimonas stu... -

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Basic information

Entry
Database: PDB / ID: 28to
Title15-subunit assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
ComponentsCyanide degrading enzyme
KeywordsHYDROLASE / Cyanide degrading enzyme / multimeric assembly / 15mer
Function / homology:
Function and homology information
Biological speciesStutzerimonas (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsDlamini, L.S. / Harrison, P. / Quigley, A. / Sewell, B.T.
Funding support South Africa, European Union, 2items
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, L.S. / Sewell, B.T.
History
DepositionFeb 18, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cyanide degrading enzyme
C: Cyanide degrading enzyme
D: Cyanide degrading enzyme
E: Cyanide degrading enzyme
F: Cyanide degrading enzyme
G: Cyanide degrading enzyme
H: Cyanide degrading enzyme
I: Cyanide degrading enzyme
J: Cyanide degrading enzyme
K: Cyanide degrading enzyme
L: Cyanide degrading enzyme
M: Cyanide degrading enzyme
N: Cyanide degrading enzyme
O: Cyanide degrading enzyme
P: Cyanide degrading enzyme


Theoretical massNumber of molelcules
Total (without water)531,02815
Polymers531,02815
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Cyanide degrading enzyme


Mass: 35401.867 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stutzerimonas (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q52445
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 14 subunit helical assembly of cyanide dihydratase from Stutzerimonas stutzeri (Pseudomonas stutzeri AK1)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 666 kDa/nm / Experimental value: YES
Source (natural)Organism: Stutzerimonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 5.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
111.2GATAN K3 BIOCONTINUUM (6k x 4k)
211.2GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategoryImage processing-IDFitting-ID
1cryoSPARCparticle selection1
4cryoSPARCCTF correction1
7PHENIXmodel fitting11
9PHENIXmodel refinement1
15ISOLDEmodel fitting2
17ISOLDEmodel refinement2
21cryoSPARC3D reconstruction1
22cryoSPARCparticle selection2
27cryoSPARC3D reconstruction2
Image processing
IDImage recording-ID
11
22
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction

Entry-ID: 28TO / Num. of particles: 857344 / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT

IDImage processing-IDAlgorithmNum. of class averages
11BACK PROJECTION
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171BACK PROJECTION1
181BACK PROJECTION
191BACK PROJECTION
201BACK PROJECTION
211BACK PROJECTION
221BACK PROJECTION
231BACK PROJECTION
241BACK PROJECTION
251BACK PROJECTION
261BACK PROJECTION
271BACK PROJECTION
281BACK PROJECTION
291BACK PROJECTION
301BACK PROJECTION
311BACK PROJECTION
321
332BACK PROJECTION
342
352
362
372
382
392
402
412
422
432
442
452
462
472
482
492BACK PROJECTION1
502BACK PROJECTION
512BACK PROJECTION
522BACK PROJECTION
532BACK PROJECTION
542BACK PROJECTION
552BACK PROJECTION
562BACK PROJECTION
572BACK PROJECTION
582BACK PROJECTION
592BACK PROJECTION
602BACK PROJECTION
612BACK PROJECTION
622BACK PROJECTION
632BACK PROJECTION
642
Atomic model building
IDProtocolSpace
1AB INITIO MODELREAL
2FLEXIBLE FIT
Atomic model building
ID 3D fitting-IDDetails (eV)Source nameType
11AutoBuild on PHENIX as used o create the initial modelOtherin silico model
22Further fitting and refinement was done using ISOLDEOtherin silico model

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