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- PDB-9er3: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a... -

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Basic information

Entry
Database: PDB / ID: 9er3
TitleCyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
ComponentsCyanide dihydratase
KeywordsHYDROLASE / Left-handed helix.
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 / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesBacillus pumilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDlamini, L.S. / Woodward, J.D. / Sewell, B.T.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
CitationJournal: To Be Published
Title: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist
Authors: Dlamini, L.S. / Woodward, J.D. / Sewell, B.T.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Cyanide dihydratase
H: Cyanide dihydratase
L: Cyanide dihydratase
B: Cyanide dihydratase
A: Cyanide dihydratase
D: Cyanide dihydratase
M: Cyanide dihydratase
F: Cyanide dihydratase
G: Cyanide dihydratase
K: Cyanide dihydratase
I: Cyanide dihydratase
C: Cyanide dihydratase
N: Cyanide dihydratase
E: Cyanide dihydratase
O: Cyanide dihydratase
P: Cyanide dihydratase
J: Cyanide dihydratase
R: Cyanide dihydratase
T: Cyanide dihydratase


Theoretical massNumber of molelcules
Total (without water)687,77619
Polymers687,77619
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 dihydratase


Mass: 36198.730 Da / Num. of mol.: 19
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: single particle reconstruction

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Sample preparation

ComponentName: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.703 MDa / Experimental value: NO
Source (natural)Organism: Bacillus pumilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 50 mM NaCL, 50 mM Tris-HCl
Buffer componentConc.: 50 mM / Name: Tris-(hydroxymethyl) aminomethane / Formula: Tris-HCl
SpecimenConc.: 1.8 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 R1.2/1.3
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.04 sec. / Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31418

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Processing

EM software
IDNameVersionCategoryDetails
1RELION4.0.1particle selection
2EPU3.5.1image acquisition
4RELION4.0.1CTF correction
7PHENIX1.2105207model fitting
10RELION4.0.1final Euler assignment
12RELION4.0.13D reconstruction
13PHENIX1.2105207model refinementreal space refine
14UCSF ChimeraX1.6.1model refinementISOLDE plugin
15Coot0.9.8.1model refinementReal space refine and rotamer fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2387974
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200866 / Algorithm: FOURIER SPACE / Num. of class averages: 50 / Symmetry type: POINT
Atomic model buildingB value: 101.248 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingDetails: The initial model was built ab initio using the map and amino acid sequence.
Source name: Other / Type: other
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00549685
ELECTRON MICROSCOPYf_angle_d0.52767469
ELECTRON MICROSCOPYf_dihedral_angle_d6.1776662
ELECTRON MICROSCOPYf_chiral_restr0.0437087
ELECTRON MICROSCOPYf_plane_restr0.0058816

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