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- EMDB-49107: Icosahedral head of Acinetobacter baumannii phage Mystique: combi... -

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Basic information

Entry
Database: EMDB / ID: EMD-49107
TitleIcosahedral head of Acinetobacter baumannii phage Mystique: combined particles
Map data
Sample
  • Virus: Mystique (virus)
    • Protein or peptide: Icosahedral head of Acinetobacter baumannii phage Mystique: combined particles
KeywordsMystique / Acinetobacter / phage / bacteriophage / VIRUS
Biological speciesMystique (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsAlseth EO / Roush C / Irby I / Kopylov M / Bobe D / Diggs M / Nguyen K / Xu H / Schmidt-Krey I / Bryksin AV / Rather PN
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: Icosahedral head of Acinetobacter baumannii phage Mystique: combined particles
Authors: Alseth EO / Roush C / Irby I / Kopylov M / Bobe D / Diggs M / Nguyen K / Xu H / Schmidt-Krey I / Bryksin AV / Rather PN
History
DepositionFeb 7, 2025-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49107.png

Downloads & links

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Map

FileDownload / File: emd_49107.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 640 pix.
= 1108.992 Å		1.73 Å/pix.
x 640 pix.
= 1108.992 Å		1.73 Å/pix.
x 640 pix.
= 1108.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.537
Minimum - Maximum-0.30867645 - 1.465635
Average (Standard dev.)0.013877472 (±0.12475196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1108.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49107_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_49107_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49107_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49107_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mystique

EntireName: Mystique (virus)
Components
  • Virus: Mystique (virus)
    • Protein or peptide: Icosahedral head of Acinetobacter baumannii phage Mystique: combined particles

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Supramolecule #1: Mystique

SupramoleculeName: Mystique / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 38018 / Sci species name: Mystique / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: AB5075

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Macromolecule #1: Icosahedral head of Acinetobacter baumannii phage Mystique: combi...

MacromoleculeName: Icosahedral head of Acinetobacter baumannii phage Mystique: combined particles
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MSKFQLLKPT GPKLKANELV AALTQGEREA QLRAASNLVQ DAGLLGCNVE AALAMYVEGG NGLNGLEATF QALNIPVNHQ GNEVAMACFA AATGTFMTNE GLRVLLPSLI NNLLRAVERT PIIERVDDLI FGTRMVKSNV MQKEITWDKA TNDSFKTHRI AEGANIPRRT ...String:
MSKFQLLKPT GPKLKANELV AALTQGEREA QLRAASNLVQ DAGLLGCNVE AALAMYVEGG NGLNGLEATF QALNIPVNHQ GNEVAMACFA AATGTFMTNE GLRVLLPSLI NNLLRAVERT PIIERVDDLI FGTRMVKSNV MQKEITWDKA TNDSFKTHRI AEGANIPRRT LKATQTGVNF FKTGHAIEMS YEFASNVTPD VLVPYAARIE FERSQDEHSL AVETIVNGES QDPNSINGPI KEVNLDTLDG KAGKPLRERA EGFMQWIINQ ARKGLQFDTL LVGWDTLMEL QLMFPVTNAN NTPAAGVGGI TGSGTQMASL AVKVANGVNF NLTLVITSQL TGHKLIGFRK GETLERLIKT NSQIAESERN IGNQTILYTN TIISGFTLAY GDTRTLLKWT QS

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.17 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: 1.0 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: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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