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- EMDB-60092: vibrio parahaemolyticus transcription factor ApHB -

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Basic information

Entry
Database: EMDB / ID: EMD-60092
Titlevibrio parahaemolyticus transcription factor ApHB
Map data
Sample
  • Complex: vibrio parahaemolyticus AphB transcription factor
KeywordsLysR / AphB / vibrio parahaemolyticus / transcription factor / DNA binding / TRANSCRIPTION
Biological speciesVibrio parahaemolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsWang HC / Chang YC / Lin SJ / Huang HJ
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)112-2628-B-038-011 Taiwan
CitationJournal: To Be Published
Title: vibrio parahaemolyticus transcription factor ApHB
Authors: Wang HC / Lin SJ
History
DepositionMay 10, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60092.png

Downloads & links

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Map

FileDownload / File: emd_60092.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.42350248 - 0.47186992
Average (Standard dev.)0.0015535494 (±0.01819503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60092_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_60092_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 : vibrio parahaemolyticus AphB transcription factor

EntireName: vibrio parahaemolyticus AphB transcription factor
Components
  • Complex: vibrio parahaemolyticus AphB transcription factor

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Supramolecule #1: vibrio parahaemolyticus AphB transcription factor

SupramoleculeName: vibrio parahaemolyticus AphB transcription factor / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio parahaemolyticus (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: 8
GridMesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 273 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 786376
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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