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- EMDB-4054: bacteriophage phi812K1-420 major capsid protein -

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Basic information

Entry
Database: EMDB / ID: 4054
Titlebacteriophage phi812K1-420 major capsid protein
SampleStaphylococcus phage 812
SourceStaphylococcus phage 812 / virus
Map databacteriophage phi812K1-420 cement protein
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsNovacek J / Siborova M / Benesik M / Pantucek R / Doskar J / Plevka P
CitationProc. Natl. Acad. Sci. U.S.A., 2016, 113, 9351-9356

Proc. Natl. Acad. Sci. U.S.A., 2016, 113, 9351-9356 Yorodumi Papers
Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate.
Jiří Nováček / Marta Šiborová / Martin Benešík / Roman Pantůček / Jiří Doškař / Pavel Plevka

Validation ReportPDB-ID: 5lij

SummaryFull reportAbout validation report
DateDeposition: Jul 14, 2016 / Header (metadata) release: Jul 26, 2017 / Map release: Jul 26, 2017 / Last update: Jul 26, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5lij
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_4054.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
1.38 Å/pix.
= 88.32 Å
64 pix
1.38 Å/pix.
= 88.32 Å
64 pix
1.38 Å/pix.
= 88.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.38 Å
Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-6.1688185 - 10.184282
Average (Standard dev.)2.294974E-9 (0.625)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 88.32 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z88.32088.32088.320
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-6.16910.1840.000

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Supplemental data

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Sample components

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Entire Staphylococcus phage 812

EntireName: Staphylococcus phage 812 / Number of components: 2

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Component #1: virus, Staphylococcus phage 812

VirusName: Staphylococcus phage 812 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Staphylococcus phage 812 / virus / Strain: K420
Source (natural)Host Species: Staphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌

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Component #2: protein, polyalanine chain built in bacteriophage phi812K1-420 ce...

ProteinName: polyalanine chain built in bacteriophage phi812K1-420 cement protein density map
Recombinant expression: No
MassTheoretical: 10.821817 kDa
Source (engineered)Expression System: Staphylococcus phage 812 / virus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 12018
3D reconstructionAlgorithm: FOURIER SPACE / Software: j3dr / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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