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- EMDB-60969: Raw consensus map of Lactobacillus casei DdmDE bound with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-60969
TitleRaw consensus map of Lactobacillus casei DdmDE bound with DNA
Map data
Sample
  • Complex: Lactobacillus casei DdmDE bound with DNA
KeywordsAgo / DNA BINDING PROTEIN / Helicase / Nuclease
Biological speciesLacticaseibacillus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsHuang PP / Chen MR / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: The mechanism of bacterial defense system DdmDE from Lactobacillus casei.
Authors: Pingping Huang / Purui Yan / Lijie Guo / Wenying Fei / Zhaoxing Li / Jingxian Liu / Jianping Kong / Yue Yao / Meiling Lu / Yibei Xiao / Meirong Chen /
History
DepositionJul 28, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60969.png

Downloads & links

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Map

FileDownload / File: emd_60969.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3300582 - 0.60420954
Average (Standard dev.)0.0008508762 (±0.014140205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60969_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_60969_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 : Lactobacillus casei DdmDE bound with DNA

EntireName: Lactobacillus casei DdmDE bound with DNA
Components
  • Complex: Lactobacillus casei DdmDE bound with DNA

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Supramolecule #1: Lactobacillus casei DdmDE bound with DNA

SupramoleculeName: Lactobacillus casei DdmDE bound with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lacticaseibacillus (bacteria)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94045
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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