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- EMDB-42680: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 -

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Basic information

Entry
Database: EMDB / ID: EMD-42680
TitleCryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43
Map datadeepenhancer map
Sample
  • Complex: Tetrameric GH43 structure
    • Protein or peptide: Beta-xylosidase
  • Ligand: CALCIUM ION
KeywordsGH43 / Enterobacter / Beta-Xylosidase / EcXyl43 / HYDROLASE
Function / homologyBeta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Beta-xylosidase
Function and homology information
Biological speciesEnterobacter hormaechei (CDC Enteric Group 75)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsBriganti L / Godoy AS / Capetti CCM / Portugal RV / Polikarpov I
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43
Authors: Briganti L / Godoy AS / Polikarpov I
History
DepositionNov 8, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42680.png

Downloads & links

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Map

FileDownload / File: emd_42680.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdeepenhancer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.015794883 - 1.594079
Average (Standard dev.)0.0019094717 (±0.03095262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryosparc refinement map

Fileemd_42680_additional_1.map
Annotationcryosparc refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: mask

Fileemd_42680_additional_2.map
Annotationmask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_42680_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_42680_half_map_2.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric GH43 structure

EntireName: Tetrameric GH43 structure
Components
  • Complex: Tetrameric GH43 structure
    • Protein or peptide: Beta-xylosidase
  • Ligand: CALCIUM ION

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Supramolecule #1: Tetrameric GH43 structure

SupramoleculeName: Tetrameric GH43 structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Enterobacter hormaechei (CDC Enteric Group 75)

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Macromolecule #1: Beta-xylosidase

MacromoleculeName: Beta-xylosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Enterobacter hormaechei (CDC Enteric Group 75)
Molecular weightTheoretical: 61.000953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEITNPILTG FNPDPSLCRQ GEDYYIATST FEWFPGVRIY HSRDLKNWTL VSTPLDRVSM LDMKGNPDSG GIWAPCLSYA DGKFWLLYT DVKIVDSPWK NGRNFLVTAP SIEGPWSEPI PMGNGGFDPS LFHDDDGRKY YLYRPWGPRH HSNPHNTIVM Q EFDPQTGT ...String:
MEITNPILTG FNPDPSLCRQ GEDYYIATST FEWFPGVRIY HSRDLKNWTL VSTPLDRVSM LDMKGNPDSG GIWAPCLSYA DGKFWLLYT DVKIVDSPWK NGRNFLVTAP SIEGPWSEPI PMGNGGFDPS LFHDDDGRKY YLYRPWGPRH HSNPHNTIVM Q EFDPQTGT LSPERKTLFT GTPLCYTEGA HLYRHAGWYY LMVAEGGTSY EHAVVVLRAK TIDGPYELHP DVTMMTSWHL PE NPLQKSG HGSLLQTHTG EWYMAYLTSR PLRLPGVPLL ASGGRGYCPL GRETGIARIE WRDGWPYVEG GKHAQLTVKG PQV AEQPAA VQGSWRDDFD GSTLDPELQT LRIPFDDTLG SLTARPGYLR LYGNDSLNST FTQSTVARRW QHFIFRAETR MQFS PVHFQ QSAGLTCYYN SKNWSYCFVD YEEGQGRTIK VIQLDHNVPS WPLHEQPIPV PEQAESVWLR VDVDRLVYRY SYSFD GETW HAVPVTYEAW KLSDDYIGGR GFFTGAFVGL HCEDISGDGC HADFDYFTYE PA

UniProtKB: Beta-xylosidase

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 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: FEI FALCON III (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7k1r

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 438836
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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