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- EMDB-36944: the alpha-galactosidase 5 with inhibitor ABP2 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36944
Titlethe alpha-galactosidase 5 with inhibitor ABP2
Map datathis is the map of alpha-galactosidases 5 with ABP2.
Sample
  • Complex: Tetramer complex of alpha-galactosidase 5 with ABP2
    • Protein or peptide: Alpha-galactosidase
  • Ligand: 8-azido-1-((1S,2S,3S,4S,5R,6S)-2,3,4-trihydroxy-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptan-7-yl)octan-1-one
Keywordsalpha-galactosidase / HYDROLASE / inhibitor ABP2
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsLi YW / Ru YX
Funding support China, 1 items
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 YW / Ru YX
History
DepositionJul 27, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36944.png

Downloads & links

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Map

FileDownload / File: emd_36944.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is the map of alpha-galactosidases 5 with ABP2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.09243086 - 0.15547863
Average (Standard dev.)0.0007097897 (±0.009346951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 184.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: this is half map 1.

Fileemd_36944_half_map_1.map
Annotationthis is half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: this is half map 2.

Fileemd_36944_half_map_2.map
Annotationthis is half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetramer complex of alpha-galactosidase 5 with ABP2

EntireName: Tetramer complex of alpha-galactosidase 5 with ABP2
Components
  • Complex: Tetramer complex of alpha-galactosidase 5 with ABP2
    • Protein or peptide: Alpha-galactosidase
  • Ligand: 8-azido-1-((1S,2S,3S,4S,5R,6S)-2,3,4-trihydroxy-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptan-7-yl)octan-1-one

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Supramolecule #1: Tetramer complex of alpha-galactosidase 5 with ABP2

SupramoleculeName: Tetramer complex of alpha-galactosidase 5 with ABP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Blautia pseudococcoides (bacteria)

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Macromolecule #1: Alpha-galactosidase

MacromoleculeName: Alpha-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Blautia pseudococcoides (bacteria)
Molecular weightTheoretical: 88.017266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVIFHEKTK EFHIFNREVS YLMRIMENGQ LENLYYGKVI RDKEDFGYLH EEAMRSQMSV CIPEPGILSM QYTRQEYPVY GTGDYRSPA LTVLQENGSR LVDFSYVSHE IYKGKKGIPP LPSTYAESED EAETLEVTLH DQVTDTDLVL TYTIYEDYPV I TRNARFEQ ...String:
MAVIFHEKTK EFHIFNREVS YLMRIMENGQ LENLYYGKVI RDKEDFGYLH EEAMRSQMSV CIPEPGILSM QYTRQEYPVY GTGDYRSPA LTVLQENGSR LVDFSYVSHE IYKGKKGIPP LPSTYAESED EAETLEVTLH DQVTDTDLVL TYTIYEDYPV I TRNARFEQ KGEQKIVLER AMSASVEFLD MDYELVQLSG AWSRERYVKN RKLEMGIQSV HSLNGTCGGA EHNPFIALKR PQ TTENQGE VYGFSLVYSG NFLAQAEVST FDMTRVMLGI NPEDFSWELN QGESFQTPEV VMVYSDRGLN KMSQAYHRLY RTR LMRVTW RDKARPILLN NWEATYFDFN EEKILKIAEK AKEAGVELFV LDDGWFGARN DDYRGLGDWY VNLEKLPDGI AGLS RKVEA LGLKFGLWVE LEMVNKDSDL YRAHPDWLIG APDRFESHAR HQHVLDFSRK EVVDYIYKMI AKVLRESSIS YIKWD MNRY MTEPYSRGAD ASQQGKVMHK YILGVYDLYT RLTTEFPEIL FESCASGGAR FDPAMLYFAP QTWTSDDTDA SERTKI QYG TSYVYPVVSM GSHVSAVPNH QMHRMTPIET RANVAYFGTF GYELDLNLLS EAELESVKKQ IAFMKEYREL IQVDGDF YR LLSPFEGNET AWMVVAQDKS RAVAAFYQRM NKVNASWIRF KLQGLDAGTL YEVSCDMAPS ASYDESLAKI YGIQTEEN M VKTYRAYGDE LMQVGIPIDR EDLNKKGGDF ASLLYTLKKV TD

UniProtKB: Alpha-galactosidase

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Macromolecule #2: 8-azido-1-((1S,2S,3S,4S,5R,6S)-2,3,4-trihydroxy-5-(hydroxymethyl)...

MacromoleculeName: 8-azido-1-((1S,2S,3S,4S,5R,6S)-2,3,4-trihydroxy-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptan-7-yl)octan-1-one
type: ligand / ID: 2 / Number of copies: 4 / Formula: VQX
Molecular weightTheoretical: 342.391 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240999
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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