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- EMDB-19910: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19910
TitleCyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
Map data
Sample
  • Organelle or cellular component: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
    • Protein or peptide: Cyanide dihydratase
KeywordsLeft-handed helix. / HYDROLASE
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 superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesBacillus pumilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDlamini LS / Woodward JD / Sewell BT
Funding support South Africa, 1 items
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 LS / Woodward JD / Sewell BT
History
DepositionMar 22, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19910.png

Downloads & links

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Map

FileDownload / File: emd_19910.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.034
Minimum - Maximum-0.059854407 - 0.111659996
Average (Standard dev.)0.00024189324 (±0.006618271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19910_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_19910_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 : Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a...

EntireName: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
Components
  • Organelle or cellular component: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
    • Protein or peptide: Cyanide dihydratase

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Supramolecule #1: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a...

SupramoleculeName: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 703 KDa

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Macromolecule #1: Cyanide dihydratase

MacromoleculeName: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 36.19873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TSIYPKFRAA AVQAAPIYLN LEASVEKSCE LIDEAASNGA KLVAFPEAFL PGYPWFAFIG HPEYTRKFYH ELYKNAVEIP SLAIQKISE AAKRNETYVC ISCSEKDGGS LYLAQLWFNP NGDLIGKHRK MRASVAERLI WGDGSGSMMP VFQTRIGNLG G LMCWEHQV ...String:
TSIYPKFRAA AVQAAPIYLN LEASVEKSCE LIDEAASNGA KLVAFPEAFL PGYPWFAFIG HPEYTRKFYH ELYKNAVEIP SLAIQKISE AAKRNETYVC ISCSEKDGGS LYLAQLWFNP NGDLIGKHRK MRASVAERLI WGDGSGSMMP VFQTRIGNLG G LMCWEHQV PLDLMAMNAQ NEQVHVASWP GYFDDEISSR YYAIATQTFV LMTSSIYTEE MKEMICLTQE QRDYFETFKS GH TCIYGPD GEPISDMVPA ETEGIAYAEI DVERVIDYKY YIDPAGHYSN QSLSMNFNQQ PTPVVKHLNH QKNEVFTYED IQ

UniProtKB: Cyanide dihydratase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.4 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl / Component - Name: Tris-(hydroxymethyl) aminomethane / Details: 50 mM NaCL, 50 mM Tris-HCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 2.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 31418 / Average exposure time: 2.04 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
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

Particle selectionNumber selected: 2387974
Startup modelType of model: NONE / Details: Initial model built ab initio
Final reconstructionNumber classes used: 50 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 200866
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationNumber classes: 50
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other
Details: The initial model was built ab initio using the map and amino acid sequence.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 101.248 / Target criteria: Cross-correlation coefficient
Output model

PDB-9er3:
Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.

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