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- PDB-12rj: Cryo-EM structure of a novel beta-galactosidase (EiGH116) from an... -

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Basic information

Entry
Database: PDB / ID: 12rj
TitleCryo-EM structure of a novel beta-galactosidase (EiGH116) from animal gut
ComponentsGlycosyl hydrolase family 116
KeywordsHYDROLASE / Glycosil
Biological speciesmetagenome (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.23 Å
AuthorsCiol, H. / Noske, G.D. / Stoffel, F. / Morao, L.G. / Martins, M.P. / Murakami, M.T.
Funding support Brazil, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/09386-8 Brazil
Sao Paulo Research Foundation (FAPESP)2022/03059-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303898/2024-0 Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of a novel beta-galactosidase (EiGH116) from animal gut
Authors: Ciol, H. / Noske, G.D. / Stoffel, F. / Morao, L.G. / Martins, M.P. / Murakami, M.T.
History
DepositionApr 15, 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

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Assembly

Deposited unit
A: Glycosyl hydrolase family 116
B: Glycosyl hydrolase family 116


Theoretical massNumber of molelcules
Total (without water)171,9392
Polymers171,9392
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 Glycosyl hydrolase family 116


Mass: 85969.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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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: Epilactase EiGH116 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.171 MDa / Experimental value: YES
Source (natural)Organism: metagenome (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 2700 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2088909 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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