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- EMDB-57206: E. coli beta-galactosidase with galacto-cyclophellitol -

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Basic information

Entry
Database: EMDB / ID: EMD-57206
TitleE. coli beta-galactosidase with galacto-cyclophellitol
Map data
Sample
  • Complex: E. coli beta-Galactosidase in a covalent complex with galacto-cyclophellitol
    • Protein or peptide: Beta-galactosidase
  • Ligand: MAGNESIUM ION
  • Ligand: (1S,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
  • Ligand: water
KeywordsBETA-GALACTOSIDASE / COMPLEX / ACTIVITY-BASED PROBE / 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: 2.7 Å
AuthorsPham PT / Alzahrani MM / Agirre J
Funding support Saudi Arabia, United Kingdom, 2 items
OrganizationGrant numberCountry
Other government Saudi Arabia
Royal Society201043 United Kingdom
CitationJournal: To Be Published
Title: E. coli beta-galactosidase with galacto-cyclophellitol
Authors: Alzahrani MM / Pham PT / Agirre J
History
DepositionMar 16, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57206.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 450 pix.
= 400.4 Å		0.89 Å/pix.
x 450 pix.
= 400.4 Å		0.89 Å/pix.
x 450 pix.
= 400.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88978 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.048946463 - 0.13685182
Average (Standard dev.)0.000097905475 (±0.0060399263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 400.40012 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57206_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_57206_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57206_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 : E. coli beta-Galactosidase in a covalent complex with galacto-cyc...

EntireName: E. coli beta-Galactosidase in a covalent complex with galacto-cyclophellitol
Components
  • Complex: E. coli beta-Galactosidase in a covalent complex with galacto-cyclophellitol
    • Protein or peptide: Beta-galactosidase
  • Ligand: MAGNESIUM ION
  • Ligand: (1S,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
  • Ligand: water

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Supramolecule #1: E. coli beta-Galactosidase in a covalent complex with galacto-cyc...

SupramoleculeName: E. coli beta-Galactosidase in a covalent complex with galacto-cyclophellitol
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 116 KDa

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Macromolecule #1: Beta-galactosidase

MacromoleculeName: Beta-galactosidase / type: protein_or_peptide / ID: 1
Details: adapted from the sequence of PDB accession code 4V40
Number of copies: 4 / Enantiomer: LEVO / EC number: beta-galactosidase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 116.471297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TMITDSLAVV LQRRDWENPG VTQLNRLAAH PPFASWRNSE EARTDRPSQQ LRSLNGEWRF AWFPAPEAVP ESWLECDLPE ADTVVVPSN WQMHGYDAPI YTNVTYPITV NPPFVPTENP TGCYSLTFNV DESWLQEGQT RIIFDGVNSA FHLWCNGRWV G YGQDSRLP ...String:
TMITDSLAVV LQRRDWENPG VTQLNRLAAH PPFASWRNSE EARTDRPSQQ LRSLNGEWRF AWFPAPEAVP ESWLECDLPE ADTVVVPSN WQMHGYDAPI YTNVTYPITV NPPFVPTENP TGCYSLTFNV DESWLQEGQT RIIFDGVNSA FHLWCNGRWV G YGQDSRLP SEFDLSAFLR AGENRLAVMV LRWSDGSYLE DQDMWRMSGI FRDVSLLHKP TTQISDFHVA TRFNDDFSRA VL EAEVQMC GELRDYLRVT VSLWQGETQV ASGTAPFGGE IIDERGGYAD RVTLRLNVEN PKLWSAEIPN LYRAVVELHT ADG TLIEAE ACDVGFREVR IENGLLLLNG KPLLIRGVNR HEHHPLHGQV MDEQTMVQDI LLMKQNNFNA VRCSHYPNHP LWYT LCDRY GLYVVDEANI ETHGMVPMNR LTDDPRWLPA MSERVTRMVQ RDRNHPSVII WSLGNESGHG ANHDALYRWI KSVDP SRPV QYEGGGADTT ATDIICPMYA RVDEDQPFPA VPKWSIKKWL SLPGETRPLI LCEYAHAMGN SLGGFAKYWQ AFRQYP RLQ GGFVWDWVDQ SLIKYDENGN PWSAYGGDFG DTPNDRQFCM NGLVFADRTP HPALTEAKHQ QQFFQFRLSG QTIEVTS EY LFRHSDNELL HWMVALDGKP LASGEVPLDV APQGKQLIEL PELPQPESAG QLWLTVRVVQ PNATAWSEAG HISAWQQW R LAENLSVTLP AASHAIPHLT TSEMDFCIEL GNKRWQFNRQ SGFLSQMWIG DKKQLLTPLR DQFTRAPLDN DIGVSEATR IDPNAWVERW KAAGHYQAEA ALLQCTADTL ADAVLITTAH AWQHQGKTLF ISRKTYRIDG SGQMAITVDV EVASDTPHPA RIGLNCQLA QVAERVNWLG LGPQENYPDR LTAACFDRWD LPLSDMYTPY VFPSENGLRC GTRELNYGPH QWRGDFQFNI S RYSQQQLM ETSHRHLLHA EEGTWLNIDG FHMGIGGDDS WSPSVSAEFQ LSAGRYHYQL VWCQK

UniProtKB: Beta-galactosidase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: (1S,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol

MacromoleculeName: (1S,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
type: ligand / ID: 3 / Number of copies: 4 / Formula: YGX
Molecular weightTheoretical: 194.182 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 170 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
1.0 mMNaClsodium chloride
50.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 5931 / Average exposure time: 5.12 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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 / Nominal magnification: 240000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 736882
CTF correctionSoftware - Name: RELION (ver. 3.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5a1a

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 204567
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5a1a


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 74.9
Output model

PDB-29jf:
E. coli beta-galactosidase with galacto-cyclophellitol

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