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- EMDB-52244: Soft-landed and rehydrated beta-galactosidase (averaged structure) -

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Basic information

Entry
Database: EMDB / ID: EMD-52244
TitleSoft-landed and rehydrated beta-galactosidase (averaged structure)
Map dataMap of soft-landed and rehydrated beta-galactosidase (averaged structure)
Sample
  • Complex: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase
Keywordsglycoside hydrolase / HYDROLASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / Resolution: 2.9 Å
AuthorsBarrass SV / Esser TK / Mowry NJ / Eriksson L / Hruby J / Seeley LT / Drabbels M / Baker LA / Rauschenbach S / Lorenz UJ
Funding support Switzerland, United Kingdom, European Union, 6 items
OrganizationGrant numberCountry
Swiss National Science Foundation213773 Switzerland
Swiss National Science Foundation207842 Switzerland
UK Research and Innovation (UKRI)EP/V051474/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V019694/1 United Kingdom
H2020 Marie Curie Actions of the European Commission883387European Union
Wellcome Trust218482/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM Sample Preparation Using Soft-landing Electrospray Ion Beam Deposition and Laser Flash Melting
Authors: Barrass SV / Esser TK / Mowry NJ / Eriksson L / Hruby J / Seeley LT / Drabbels M / Baker LA / Rauschenbach S / Lorenz UJ
History
DepositionDec 4, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52244.png

Downloads & links

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Map

FileDownload / File: emd_52244.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of soft-landed and rehydrated beta-galactosidase (averaged structure)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 371.712 Å		0.73 Å/pix.
x 512 pix.
= 371.712 Å		0.73 Å/pix.
x 512 pix.
= 371.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0334
Minimum - Maximum-0.23378496 - 0.43585724
Average (Standard dev.)0.00008259953 (±0.005869823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of soft-landed and rehydrated beta-galactosidase...

Fileemd_52244_half_map_1.map
AnnotationHalf map A of soft-landed and rehydrated beta-galactosidase (averaged structure)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of soft-landed and rehydrated beta-galactosidase...

Fileemd_52244_half_map_2.map
AnnotationHalf map B of soft-landed and rehydrated beta-galactosidase (averaged structure)
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 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MITDSLAVVL QRRDWENPGV TQLNRLAAHP PFASWRNSEE ARTDRPSQQL RSLNGEWRFA WFPAPEAVPE SWLECDLPEA DTVVVPSNW QMHGYDAPIY TNVTYPITVN PPFVPTENPT GCYSLTFNVD ESWLQEGQTR IIFDGVNSAF HLWCNGRWVG Y GQDSRLPS ...String:
MITDSLAVVL QRRDWENPGV TQLNRLAAHP PFASWRNSEE ARTDRPSQQL RSLNGEWRFA WFPAPEAVPE SWLECDLPEA DTVVVPSNW QMHGYDAPIY TNVTYPITVN PPFVPTENPT GCYSLTFNVD ESWLQEGQTR IIFDGVNSAF HLWCNGRWVG Y GQDSRLPS EFDLSAFLRA GENRLAVMVL RWSDGSYLED QDMWRMSGIF RDVSLLHKPT TQISDFHVAT RFNDDFSRAV LE AEVQMCG ELRDYLRVTV SLWQGETQVA SGTAPFGGEI IDERGGYADR VTLRLNVENP KLWSAEIPNL YRAVVELHTA DGT LIEAEA CDVGFRVVRI ENGLLLLNGK PLLIRGVNRH EHHPLHGQVM DEQTMVQDIL LMKQNNFNAV RCSHYPNHPL WYTL CDRYG LYVVDEANIE THGMVPMNRL TDDPRWLPAM SERVTRMVQR DRNHPSVIIW SLGNESGHGA NHDALYRWIK SVDPS RPVQ YEGGGADTTA TDIICPMYAR VDEDQPFPAV PKWSIKKWLS LPGETRPLIL CEYAHAMGNS LGGFAKYWQA FRQYPR LQG GFVWDWVDQS LIKYDENGNP WSAYGGDFGD TPNDRQFCMN GLVFADRTPH PALTEAKHQQ QFFQFRLSGQ TIEVTSE YL FRHSDNELLH WMVALDGKPL ASGEVPLDVA PQGKQLIELP ELPQPESAGQ LWLTVRVVQP NATAWSEAGH ISAWQQWR L AENLSVTLPA ASHAIPHLTT SEMDFCIELG NKRWQFNRQS GFLSQMWIGD KKQLLTPLRD QFTRAPLDND IGVSEATRI DPNAWVERWK AAGHYQAEAA LLQCTADTLA DAVLITTAHA WQHQGKTLFI SRKTYRIDGS GQMAITVDVV VASDTPHPAR IGLNCQLAQ VAERVNWLGL GPQENYPDRL TAACFDRWDL PLSDMYTPYV FPSENGLRCG TRELNYGPHQ WRGDFQFNIS R YSQQQLME TSHRHLLHAE EGTWLNIDGF HMGIGGDDSW SPSVSAEFQL SAGRYHYQLV WCQ

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
DetailsBeta-galactosidase was deposited onto a cryo-EM grid using soft-landing electrospray ion beam deposition. 50 nm of amorphous ice was deposited onto the sample and laser flash melting and revitrification was used to rehydrate the protein.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 44929 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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

Particle selectionNumber selected: 4415932
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Software - details: Non-uniform refinement / Number images used: 1504908
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Software - details: ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD

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