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- PDB-8k1a: the wild-typed alpha-galactosidase 5 -

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Basic information

Entry
Database: PDB / ID: 8k1a
Titlethe wild-typed alpha-galactosidase 5
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / alpha-Galactosidase
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process
Similarity search - Function
Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Glycosyl hydrolase, all-beta ...Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Glycosyl hydrolase, all-beta / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBlautia pseudococcoides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLi, Y.W. / Ru, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentK22227503 China
CitationJournal: To Be Published
Title: Activity-Based Meta proteomics Drives Discovery and Enzymological Characterization of Novel alpha-galactosidases in the Gut Microbiome
Authors: Li, Y.W. / Ru, Y.X.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase
B: Alpha-galactosidase
C: Alpha-galactosidase
D: Alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)352,0694
Polymers352,0694
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
Alpha-galactosidase


Mass: 88017.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blautia pseudococcoides (bacteria) / Gene: A4V09_19485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C7IHX3

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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: Tetramer complex of alpha-galactosidase 5 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Blautia pseudococcoides (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94011 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424402
ELECTRON MICROSCOPYf_angle_d0.60332996
ELECTRON MICROSCOPYf_dihedral_angle_d4.8243291
ELECTRON MICROSCOPYf_chiral_restr0.0443496
ELECTRON MICROSCOPYf_plane_restr0.0044266

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