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- EMDB-56975: Beta-galactosidase from E.Coli -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56975
TitleBeta-galactosidase from E.Coli
Map data
Sample
  • Complex: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase
KeywordsBeta-galactosidase / HYDROLASE
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsZimmermann M / Braun T
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Biorxiv / Year: 2026
Title: Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material
Authors: Zimmermann M / Braun T
History
DepositionMar 2, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56975.png

Downloads & links

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Map

FileDownload / File: emd_56975.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.560563 - 0.8908158
Average (Standard dev.)0.00019986069 (±0.017393623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56975_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56975_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Beta-galactosidase

EntireName: Beta-galactosidase
Components
  • Complex: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase

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Supramolecule #1: Beta-galactosidase

SupramoleculeName: Beta-galactosidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Beta-galactosidase

MacromoleculeName: Beta-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: beta-galactosidase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 118.770805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTMITDSLAV VLQRRDWENP GVTQLNRLAA HPPFASWRNS EEARTDRPSQ QLRSLNGEWR FAWFPAPEAV PESWLECDLP EADTVVVPS NWQMHGYDAP IYTNVTYPIT VNPPFVPTEN PTGCYSLTFN VDESWLQEGQ TRIIFDGVNS AFHLWCNGRW V GYGQDSRL ...String:
MTMITDSLAV VLQRRDWENP GVTQLNRLAA HPPFASWRNS EEARTDRPSQ QLRSLNGEWR FAWFPAPEAV PESWLECDLP EADTVVVPS NWQMHGYDAP IYTNVTYPIT VNPPFVPTEN PTGCYSLTFN VDESWLQEGQ TRIIFDGVNS AFHLWCNGRW V GYGQDSRL PSEFDLSAFL RAGENRLAVM VLRWSDGSYL EDQDMWRMSG IFRDVSLLHK PTTQISDFHV ATRFNDDFSR AV LEAEVQM CGELRDYLRV TVSLWQGETQ VASGTAPFGG EIIDERGGYA DRVTLRLNVE NPKLWSAEIP NLYRAVVELH TAD GTLIEA EACDVGFREV RIENGLLLLN GKPLLIRGVN RHEHHPLHGQ VMDEQTMVQD ILLMKQNNFN AVRCSHYPNH PLWY TLCDR YGLYVVDEAN IETHGMVPMN RLTDDPRWLP AMSERVTRMV QRDRNHPSVI IWSLGNESGH GANHDALYRW IKSVD PSRP VQYEGGGADT TATDIICPMY ARVDEDQPFP AVPKWSIKKW LSLPGETRPL ILCEYAHAMG NSLGGFAKYW QAFRQY PRL QGGFVWDWVD QSLIKYDENG NPWSAYGGDF GDTPNDRQFC MNGLVFADRT PHPALTEAKH QQQFFQFRLS GQTIEVT SE YLFRHSDNEL LHWMVALDGK PLASGEVPLD VAPQGKQLIE LPELPQPESA GQLWLTVRVV QPNATAWSEA GHISAWQQ W RLAENLSVTL PAASHAIPHL TTSEMDFCIE LGNKRWQFNR QSGFLSQMWI GDKKQLLTPL RDQFTRAPLD NDIGVSEAT RIDPNAWVER WKAAGHYQAE AALLQCTADT LADAVLITTA HAWQHQGKTL FISRKTYRID GSGQMAITVD VEVASDTPHP ARIGLNCQL AQVAERVNWL GLGPQENYPD RLTAACFDRW DLPLSDMYTP YVFPSENGLR CGTRELNYGP HQWRGDFQFN I SRYSQQQL METSHRHLLH AEEGTWLNID GFHMGIGGDD SWSPSVSAEL QLSAGRYHYQ LVWCQKGSGS GSPSRLEEEL RR RLTE

UniProtKB: Beta-galactosidase

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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: 8
Details: Tris 25 mM, NaCl 50 mM, 2 mM MgCl2, 1 mM TCEP, pH 8.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Details: cryoWriter.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 8888 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 814849
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab inito model
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 218218
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-28yo:
Beta-galactosidase from E.Coli

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