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- EMDB-34618: Cryo-EM structure of Beta-galactosidase at 1.57A resolution -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-34618
TitleCryo-EM structure of Beta-galactosidase at 1.57A resolution
Map data
Sample
  • Complex: Beta-galactosidase
KeywordsBeta-galactosidase / Complex / Protein / HYDROLASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.57 Å
AuthorsHamaguchi T / Yonekura K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of Beta-galactosidase at 1.57A resolution
Authors: Hamaguchi T / Yonekura K
History
DepositionOct 27, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34618.png

Downloads & links

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Map

FileDownload / File: emd_34618.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 800 pix.
= 396. Å		0.5 Å/pix.
x 800 pix.
= 396. Å		0.5 Å/pix.
x 800 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0085
Minimum - Maximum-0.03833975 - 0.10315339
Average (Standard dev.)0.0000005365837 (±0.0020645268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34618_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_34618_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

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Supramolecule #1: Beta-galactosidase

SupramoleculeName: Beta-galactosidase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 466 KDa

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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: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
150.0 mMNaClsodium chloride
2.0 mMMgCl2magnesium chloride
1.0 mMDTTdithiothreitol
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
TemperatureMin: 90.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 5 / Number real images: 37001 / Average exposure time: 2.73 sec. / Average electron dose: 40.0 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: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 4620147
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1483327
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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