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

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Basic information

Entry
Database: PDB / ID: 8soy
TitleCryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis
ComponentsEnoyl-CoA hydratase EchA21
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Lyase
Function / homologyDelta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / enoyl-CoA hydratase / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / fatty acid beta-oxidation / ClpP/crotonase-like domain superfamily / lyase activity / Enoyl-CoA hydratase EchA21
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single 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, 1items
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, I.Q. / Barrett, L.Q. / Van Voorhis, W.C.
History
DepositionApr 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase EchA21
B: Enoyl-CoA hydratase EchA21
C: Enoyl-CoA hydratase EchA21
D: Enoyl-CoA hydratase EchA21
E: Enoyl-CoA hydratase EchA21
F: Enoyl-CoA hydratase EchA21


Theoretical massNumber of molelcules
Total (without water)158,2796
Polymers158,2796
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Enoyl-CoA hydratase EchA21


Mass: 26379.848 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: echA8_4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A653F8X5

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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: Enoyl-CoA Hydratase hexamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenConc.: 2 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: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 296 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
7PHENIX1.14model fitting
9PHENIX1.14model refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1500881 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 10.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005410236
ELECTRON MICROSCOPYf_angle_d0.72113960
ELECTRON MICROSCOPYf_chiral_restr0.05151710
ELECTRON MICROSCOPYf_plane_restr0.00721786
ELECTRON MICROSCOPYf_dihedral_angle_d5.17781500

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