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- EMDB-33519: CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33519
TitleCryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 in vitro
Map data
Sample
  • Complex: Klebsiella phage Kp7 type II tail fiber
    • Protein or peptide: phage tail fiber
KeywordsPhage type II tail fiber / VIRAL PROTEIN
Biological speciesKlebsiella phage Kp7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHuang L / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers
Authors: Huang L / Xiang Y
History
DepositionJun 1, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33519.png

Downloads & links

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Map

FileDownload / File: emd_33519.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 200 pix.
= 234. Å		1.17 Å/pix.
x 200 pix.
= 234. Å		1.17 Å/pix.
x 200 pix.
= 234. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.114270404 - 0.14933577
Average (Standard dev.)0.00025830345 (±0.0048523713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Klebsiella phage Kp7 type II tail fiber

EntireName: Klebsiella phage Kp7 type II tail fiber
Components
  • Complex: Klebsiella phage Kp7 type II tail fiber
    • Protein or peptide: phage tail fiber

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Supramolecule #1: Klebsiella phage Kp7 type II tail fiber

SupramoleculeName: Klebsiella phage Kp7 type II tail fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Trimer of tail fiber proteins
Source (natural)Organism: Klebsiella phage Kp7 (virus)

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Macromolecule #1: phage tail fiber

MacromoleculeName: phage tail fiber / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp7 (virus)
Molecular weightTheoretical: 61.21027 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MALVKATFVK DVDGQPWRFS SVAKMKAFNY SCYLGSSVFL ESWHEGAGLG SGLFKVSKGT TEVGDDGSVI VAADGTRLIR VFDGPIFAD MWGALPSSTY NSLPAIKSAY LYASSKLQQL FLGGGSYKVT GSSGIDIDPS LAGISALSRA RVDTTEFTGD Y LFTITSSY ...String:
MALVKATFVK DVDGQPWRFS SVAKMKAFNY SCYLGSSVFL ESWHEGAGLG SGLFKVSKGT TEVGDDGSVI VAADGTRLIR VFDGPIFAD MWGALPSSTY NSLPAIKSAY LYASSKLQQL FLGGGSYKVT GSSGIDIDPS LAGISALSRA RVDTTEFTGD Y LFTITSSY SYTPAPYYNN LSVALEGLYV FGNKTEGRSG LLTGRRTTDG VKSYNGQTEI RNCTFDKFDY NIRMGHNSWR IV FYKVNSL NALNANGILY VPSGLDDSGE ILTFYHCQFF DGAGSNIRIS CSSFAMTFVS CSFLNITFTI DAGSSVSVTA LGC NFENPG SQSTRRYIEI TAGHTNIFNV VGGSIVTNAN AGQTQALIHV SANNQINLSN LTIPYGAHYQ QEADSGYHAF CSGQ GYVST SNCSLQLLNG AGCCPIHPSL SVFTNWNLSY ANLNAWTVDK GSAPTSVAEY LSAQGPKGEG VLHVAPTTQG VNISQ VATV SKQAGSMSMS VMVNIISASS NAGQISLAYL DAFDNNLGGV SANLGTTTGW KVIGKNTLRG RLPVGTAKVR LNIQTV AGA DVQYTNILCN II

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 113834
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 146
Output model

PDB-7xyc:
CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 in vitro

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