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- EMDB-1996: Bubblegrams reveal the inner body of bacteriophage phiKZ -

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Basic information

Entry
Database: EMDB / ID: 1996
TitleBubblegrams reveal the inner body of bacteriophage phiKZ
Keywordsinner body / core protein / asymmetric reconstruction / phiKZ / protein mapping
SamplephiKZ mature phage
SourcePseudomonas phage phiKZ / virus / phiKZ
Map dataThis is the inner body structure of bacteriophage phiKZ.
Methodsingle particle reconstruction, at 37 Å resolution
AuthorsWu W / Thomas JA / Cheng N / Black LW / Steven AC
CitationScience, 2012, 335, 182-182

Science, 2012, 335, 182-182 Yorodumi Papers
Bubblegrams reveal the inner body of bacteriophage φKZ.
Weimin Wu / Julie A Thomas / Naiqian Cheng / Lindsay W Black / Alasdair C Steven

DateDeposition: Nov 23, 2011 / Header (metadata) release: Jan 13, 2012 / Map release: Jan 13, 2012 / Last update: Sep 26, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 750
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 750
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1996.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
10.03 Å/pix.
= 1604.16 Å
160 pix
10.03 Å/pix.
= 1604.16 Å
160 pix
10.03 Å/pix.
= 1604.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 10.026 Å
Density
Contour Level:750 (by author), 750 (movie #1):
Minimum - Maximum-5409.6 - 9004.46
Average (Standard dev.)10.7033 (238.579)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
CellA=B=C: 1604.16 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.02610.02610.026
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z1604.1601604.1601604.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-5409.5959004.45910.703

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Supplemental data

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Sample components

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Entire phiKZ mature phage

EntireName: phiKZ mature phage / Number of components: 5
Oligomeric State: Inner body inside the capsid surrounding by DNA

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Component #1: virus, Pseudomonas phage phiKZ

VirusName: Pseudomonas phage phiKZ / a.k.a: phiKZ / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Pseudomonas phage phiKZ / virus / phiKZ
Source (natural)Host Species: Pseudomonas aeruginosa / bacteria / シュードモナス・エルジノーサ, 緑膿菌
Host category: BACTERIA(EUBACTERIA)

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 40 %

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jan 20, 2011
Details: Image pairs. First low dose image, 12 electrons per angstrom squared, then high dose to get radiation damage (same dose but longer time), dose about 5-fold of low dose.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 12 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 38000 X (nominal), 38000 X (calibrated) / Astigmatism: condenser and objective lens astigmatism / Cs: 2 mm / Imaging mode: OTHER / Defocus: 800 - 1500 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 95 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2775 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection match / Software: EMAN / CTF correction: Micrograph
Details: Projection match method was used to determine the unique vertex and the orientation of tail. The inner body was solved directly from 2D data without using any initial model.
Resolution: 37 Å / Resolution method: FSC 0.5

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