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- EMDB-81969: Beta-galactosidase at 1.36 Angstrom without inhibitors -

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Basic information

Entry
Database: EMDB / ID: EMD-81969
TitleBeta-galactosidase at 1.36 Angstrom without inhibitors
Map dataCS sharp
Sample
  • Complex: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase
  • Ligand: water
KeywordsBeta-galactosidase / near atomic resolution / no inhibitor / HYDROLASE
Function / homology
Function and homology information


lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion 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: 1.36 Å
AuthorsBurton-Smith RN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Beta-galactosidase at 1.36 Angstrom
Authors: Burton-Smith RN
History
DepositionJul 7, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_81969.png

Downloads & links

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Map

FileDownload / File: emd_81969.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCS sharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.36 Å/pix.
x 800 pix.
= 289.2 Å		0.36 Å/pix.
x 800 pix.
= 289.2 Å		0.36 Å/pix.
x 800 pix.
= 289.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3615 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.4009778 - 0.928285
Average (Standard dev.)0.00015035222 (±0.010850167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 289.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_81969_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_81969_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LocResFilt (RELION from CS halfmaps)

Fileemd_81969_additional_1.map
AnnotationLocResFilt (RELION from CS halfmaps)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CS half A

Fileemd_81969_half_map_1.map
AnnotationCS half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CS half B

Fileemd_81969_half_map_2.map
AnnotationCS half B
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
  • Ligand: water

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Supramolecule #1: Beta-galactosidase

SupramoleculeName: Beta-galactosidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 115.98168 KDa
SequenceString: ITDSLAVVLQ RRDWENPGVT QLNRLAAHPP FASWRNSEEA RTDRPSQQLR SLNGEWRFAW FPAPEAVPES WLECDLPEAD TVVVPSNWQ MHGYDAPIYT NVTYPITVNP PFVPTENPTG CYSLTFNVDE SWLQEGQTRI IFDGVNSAFH LWCNGRWVGY G QDSRLPSE ...String:
ITDSLAVVLQ RRDWENPGVT QLNRLAAHPP FASWRNSEEA RTDRPSQQLR SLNGEWRFAW FPAPEAVPES WLECDLPEAD TVVVPSNWQ MHGYDAPIYT NVTYPITVNP PFVPTENPTG CYSLTFNVDE SWLQEGQTRI IFDGVNSAFH LWCNGRWVGY G QDSRLPSE FDLSAFLRAG ENRLAVMVLR WSDGSYLEDQ DMWRMSGIFR DVSLLHKPTT QISDFHVATR FNDDFSRAVL EA EVQMCGE LRDYLRVTVS LWQGETQVAS GTAPFGGEII DERGGYADRV TLRLNVENPK LWSAEIPNLY RAVVELHTAD GTL IEAEAC DVGFREVRIE NGLLLLNGKP LLIRGVNRHE HHPLHGQVMD EQTMVQDILL MKQNNFNAVR CSHYPNHPLW YTLC DRYGL YVVDEANIET HGMVPMNRLT DDPRWLPAMS ERVTRMVQRD RNHPSVIIWS LGNESGHGAN HDALYRWIKS VDPSR PVQY EGGGADTTAT DIICPMYARV DEDQPFPAVP KWSIKKWLSL PGETRPLILC EYAHAMGNSL GGFAKYWQAF RQYPRL QGG FVWDWVDQSL IKYDENGNPW SAYGGDFGDT PNDRQFCMNG LVFADRTPHP ALTEAKHQQQ FFQFRLSGQT IEVTSEY LF RHSDNELLHW MVALDGKPLA SGEVPLDVAP QGKQLIELPE LPQPESAGQL WLTVRVVQPN ATAWSEAGHI SAWQQWRL A ENLSVTLPAA SHAIPHLTTS EMDFCIELGN KRWQFNRQSG FLSQMWIGDK KQLLTPLRDQ FTRAPLDNDI GVSEATRID PNAWVERWKA AGHYQAEAAL LQCTADTLAD AVLITTAHAW QHQGKTLFIS RKTYRIDGSG QMAITVDVEV ASDTPHPARI GLNCQLAQV AERVNWLGLG PQENYPDRLT AACFDRWDLP LSDMYTPYVF PSENGLRCGT RELNYGPHQW RGDFQFNISR Y SQQQLMET SHRHLLHAEE GTWLNIDGFH MGIGGDDSWS PSVSAEFQLS AGRYHYQLVW C

UniProtKB: Beta-galactosidase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1416 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 12 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1489271
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-43ls:
Beta-galactosidase (without inhibitors) (E. coli)

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