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- EMDB-37333: Structure of DegQ-b-casein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37333
TitleStructure of DegQ-b-casein complex
Map data
Sample
  • Complex: DegQ-beta casein complex
KeywordsComplex / HYDROLASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 Å
AuthorsLee I-G / Jeon H
Funding support1 items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02
CitationJournal: To Be Published
Title: Structure of E. coli Deg-b-casein complex
Authors: Lee I-G / Jeon H
History
DepositionAug 29, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37333.png

Downloads & links

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Map

FileDownload / File: emd_37333.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.44 Å/pix.
x 720 pix.
= 314.46 Å		0.44 Å/pix.
x 720 pix.
= 314.46 Å		0.44 Å/pix.
x 720 pix.
= 314.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.43675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0101
Minimum - Maximum-0.016317101 - 0.042638335
Average (Standard dev.)0.000098213655 (±0.0022034815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 314.46 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37333_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_37333_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 : DegQ-beta casein complex

EntireName: DegQ-beta casein complex
Components
  • Complex: DegQ-beta casein complex

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Supramolecule #1: DegQ-beta casein complex

SupramoleculeName: DegQ-beta casein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3stj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73850
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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