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- EMDB-3604: Structure of the C. crescentus S-layer -

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Basic information

Entry
Database: EMDB / ID: 3604
TitleStructure of the C. crescentus S-layer
SampleCaulobacter crescentus S-layer
SourceCaulobacter crescentus na1000 / bacteria
Map dataSub-tomogram averaging of the Caulobacter crescentus S-layer
Methodsubtomogram averaging, at 7.4 A resolution
AuthorsBharat TA / Hagen WJ
CitationTo Be Published

To Be Published Search PubMed
Structure of the C. crescentus S-layer
Bharat TA / Lowe J

DateDeposition: Feb 24, 2017 / Header (metadata) release: Mar 29, 2017 / Map release: Apr 19, 2017 / Last update: Feb 24, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5n97
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3604.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.35 A/pix
= 270. A
200 pix
1.35 A/pix
= 270. A
200 pix
1.35 A/pix
= 270. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 A
Density
Contour Level:0.11 (by author), 0.11 (movie #1):
Minimum - Maximum-0.25166476 - 0.5049828
Average (Standard dev.)-0.009878825 (0.0565414)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 270 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.351.351.35
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z270.000270.000270.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2520.505-0.010

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Supplemental data

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Sample components

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Entire Caulobacter crescentus S-layer

EntireName: Caulobacter crescentus S-layer / Details: Caulobacter crescentus S-layer / Number of components: 3

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Component #1: cellular-component, Caulobacter crescentus S-layer

Cellular-componentName: Caulobacter crescentus S-layer / Details: Caulobacter crescentus S-layer / Recombinant expression: No
SourceSpecies: Caulobacter crescentus na1000 / bacteria / Strain: YB2811
Source (natural)Location in cell: extra-cellular

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Component #2: protein, S-layer protein rsaA

ProteinName: S-layer protein rsaA / Recombinant expression: No
MassTheoretical: 73.159305 kDa
SourceSpecies: Caulobacter crescentus na1000 / bacteria

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Component #3: ligand, CALCIUM ION

LigandName: CALCIUM ION / Number of Copies: 114 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: PYE medium / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283.15 K / Humidity: 100 % / Details: 1.5 s blot

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.4 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal), 105000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm / Energy filter: Gatan Quantum / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg. / Temperature: K ( 70 - 70 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: Dose symmetric tilt scheme (Hagen et al)

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Image processing

ProcessingMethod: subtomogram averaging
3D reconstructionAlgorithm: FOURIER SPACE / CTF correction: Following Schur et al, 2016 / Resolution: 7.4 A / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Following Schur et al, 2016

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Atomic model buiding

Output model

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