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- EMDB-40671: Cryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: EMD-40671
TitleCryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis
Map data
Sample
  • Complex: Enoyl-CoA Hydratase hexamer
    • Protein or peptide: Enoyl-CoA hydratase EchA21
KeywordsStructural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Lyase / HYDROLASE
Function / homologyDelta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / fatty acid beta-oxidation / isomerase activity / ClpP/crotonase-like domain superfamily / Putative enoyl-CoA hydratase echA8
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsShek R / Quispe J / Staker B / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis
Authors: Shek R / Quispe J / Staker B / Phan IQ / Barrett LQ / Van Voorhis WC
History
DepositionApr 30, 2023-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40671.png

Downloads & links

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Map

FileDownload / File: emd_40671.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 276 pix.
= 237.36 Å		0.86 Å/pix.
x 276 pix.
= 237.36 Å		0.86 Å/pix.
x 276 pix.
= 237.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-4.255125 - 5.754695
Average (Standard dev.)0.002896357 (±0.15911594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions276276276
Spacing276276276
CellA=B=C: 237.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40671_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_40671_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 : Enoyl-CoA Hydratase hexamer

EntireName: Enoyl-CoA Hydratase hexamer
Components
  • Complex: Enoyl-CoA Hydratase hexamer
    • Protein or peptide: Enoyl-CoA hydratase EchA21

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Supramolecule #1: Enoyl-CoA Hydratase hexamer

SupramoleculeName: Enoyl-CoA Hydratase hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: Enoyl-CoA hydratase EchA21

MacromoleculeName: Enoyl-CoA hydratase EchA21 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 26.379848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YESVTVEVKD HVAQVTLIGP GKGNAMGPAF WEEMPDVFGT LDDDPDVRAI VLTGSGKNFS YGLDLPAMGA SLPALDAGAK SRSDFHKRL QKMQGAITAV ADCRTPTIAS VHGWCIGGGV DLISAVDIRY ASADAKFSVR EVKLAIVADV GSLARLPLIL S DGHLRELA ...String:
YESVTVEVKD HVAQVTLIGP GKGNAMGPAF WEEMPDVFGT LDDDPDVRAI VLTGSGKNFS YGLDLPAMGA SLPALDAGAK SRSDFHKRL QKMQGAITAV ADCRTPTIAS VHGWCIGGGV DLISAVDIRY ASADAKFSVR EVKLAIVADV GSLARLPLIL S DGHLRELA LTGKDIDAAR AEKIGLVNDV YDDAEASLAA AHATAAEIAA NPPLTVAGVK DVLDAQRTAQ VAESLRYVAA WN SAFLPSK DLAEA

UniProtKB: Putative enoyl-CoA hydratase echA8

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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

Concentration2 mg/mL
BufferpH: 7
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 1500881
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8soy:
Cryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis

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