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- PDB-8p4i: Cyanide dihydratase from Bacillus pumilus C1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8p4i
TitleCyanide dihydratase from Bacillus pumilus C1
ComponentsCyanide dihydratase
KeywordsHYDROLASE / Cyanide degrading enzyme
Function / homology
Function and homology information


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 / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus pumilus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsMulelu, A.E. / Reitz, J. / van Rooyen, J.M. / Scheffer, M. / Frangakis, A.S. / Dlamini, L.S. / Woodward, J.D. / Benedik, M.J. / Sewell, B.T.
Funding support South Africa, 1items
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, A.E. / Reitz, J. / van Rooyen, J. / Scheffer, M. / Frangakis, A.S. / Dlamini, L.S. / Woodward, J.D. / Benedik, M.J. / Sewell, B.T.
History
DepositionMay 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: 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 dihydratase
D: Cyanide dihydratase
F: Cyanide dihydratase
G: Cyanide dihydratase
H: Cyanide dihydratase
I: Cyanide dihydratase
J: Cyanide dihydratase
K: Cyanide dihydratase
L: Cyanide dihydratase
M: Cyanide dihydratase
N: Cyanide dihydratase
O: Cyanide dihydratase
P: Cyanide dihydratase
Q: Cyanide dihydratase
R: Cyanide dihydratase
S: Cyanide dihydratase
U: Cyanide dihydratase


Theoretical massNumber of molelcules
Total (without water)611,00417
Polymers611,00417
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79630 Å2
ΔGint-438 kcal/mol
Surface area205790 Å2

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Components

#1: Protein
Cyanide dihydratase


Mass: 35941.418 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: cynD / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GGL4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Wildtype cyanide dihydratase from Bacillus pumilus C1 / Type: COMPLEX
Details: Homo-oligomeric 18mer expressed recombinantly without a purification tag.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.666 kDa/nm / Experimental value: YES
Source (natural)Organism: Bacillus pumilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 5.4
Buffer componentConc.: 50 mM / Name: citrate / Formula: C6H8O7
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 59.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
7Coot0.98.1model fitting
19PHENIX1.2model refinementPHENIX was used to generate a model with better fit into the map
20UCSF ChimeraX1.4model refinementThe ISOLDE plugin of UCSF ChimeraX was used for further model fitting into the map and obtaining correct geometry
21Coot0.98.1model refinementCoot was used to obtain correct residue geometry
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -77 ° / Axial rise/subunit: 16.9 Å / Axial symmetry: C2
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 120943 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00344132
ELECTRON MICROSCOPYf_angle_d0.53359925
ELECTRON MICROSCOPYf_dihedral_angle_d4.195865
ELECTRON MICROSCOPYf_chiral_restr0.0426290
ELECTRON MICROSCOPYf_plane_restr0.0047820

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