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- PDB-38lb: Cryo EM structure of a formate acetyltransferase (PFL) from Fanny... -

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Basic information

Entry
Database: PDB / ID: 38lb
TitleCryo EM structure of a formate acetyltransferase (PFL) from Fannyhessea vaginae
ComponentsFormate acetyltransferase
KeywordsLYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / formate acetyltransferase (PFL) / Fannyhessea vaginae
Function / homology
Function and homology information


formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / cytosol
Similarity search - Function
Formate acetyltransferase / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain
Similarity search - Domain/homology
Formate acetyltransferase
Similarity search - Component
Biological speciesFannyhessea vaginae DSM 15829 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.18 Å
AuthorsLiu, L. / Lovell, S. / Hammons, A.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD036339 United States
CitationJournal: To be published
Title: Cryo EM structure of a formate acetyltransferase (PFL) from Fannyhessea vaginae
Authors: Liu, L. / Lovell, S. / Hammons, A.M.
History
DepositionSep 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formate acetyltransferase
B: Formate acetyltransferase
C: Formate acetyltransferase
D: Formate acetyltransferase


Theoretical massNumber of molelcules
Total (without water)333,8934
Polymers333,8934
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
Formate acetyltransferase / Pyruvate formate-lyase


Mass: 83473.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fannyhessea vaginae DSM 15829 (bacteria)
Gene: pflB, HMPREF0091_10019 / Plasmid: FavaA.20507.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F1T4Y4, formate C-acetyltransferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tetramer of formate acetyltransferase (PFL) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.333 MDa / Experimental value: YES
Source (natural)Organism: Fannyhessea vaginae DSM 15829 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: FavaA.20507.a.A1
Buffer solutionpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
SpecimenConc.: 1 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: VITREOUS ICE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal magnification: 100000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 400 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON I (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6168
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5particle selection
2EPUimage acquisition
4cryoSPARC5CTF correction
7UCSF ChimeraX1.12model fitting
9PHENIX2.0_5936model refinement
10cryoSPARC5initial Euler assignment
11cryoSPARC5classification
12cryoSPARC53D reconstruction
Image processingDetails: The selected images were high-pass filtered and normalized
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7673418
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1554278 / Algorithm: FOURIER SPACE / Num. of class averages: 15 / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingAccession code: AF-F1T4Y4-F1 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.18 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219696
ELECTRON MICROSCOPYf_angle_d0.3826612
ELECTRON MICROSCOPYf_dihedral_angle_d4.012688
ELECTRON MICROSCOPYf_chiral_restr0.0372848
ELECTRON MICROSCOPYf_plane_restr0.0033440

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