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- EMDB-1605: Solution structure of the KdpFABC P-type ATPase from Escherichia ... -

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Basic information

Entry
Database: EMDB / ID: 1605
TitleSolution structure of the KdpFABC P-type ATPase from Escherichia coli by electron microscopic single particle analysis
KeywordsKdpFABC / P-type ATPase / potassium transport / single particle analysis / electron microscopy.
SampleKdpFABC P-type ATPase
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataVolume of the KdpFABC P-type ATPase
Methodsingle particle reconstruction, at 19 Å resolution
AuthorsHeitkamp T / Bottcher B / Greie J-C
CitationJ. Struct. Biol., 2009, 166, 295-302

J. Struct. Biol., 2009, 166, 295-302 Yorodumi Papers
Solution structure of the KdpFABC P-type ATPase from Escherichia coli by electron microscopic single particle analysis.
Thomas Heitkamp / Bettina Böttcher / Jörg-Christian Greie

DateDeposition: Mar 17, 2009 / Header (metadata) release: Apr 15, 2009 / Map release: Apr 24, 2009 / Last update: Oct 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 200
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 200
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1605.map.gz (map file in CCP4 format, 1341 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
70 pix
2.8 Å/pix.
= 196. Å
70 pix
2.8 Å/pix.
= 196. Å
70 pix
2.8 Å/pix.
= 196. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:150 (by author), 200 (movie #1):
Minimum - Maximum-374.723 - 1448.24
Average (Standard dev.)15.9693 (95.5698)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions707070
Origin000
Limit696969
Spacing707070
CellA=B=C: 196 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z196.000196.000196.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-374.7231448.24115.969

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Supplemental data

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Sample components

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Entire KdpFABC P-type ATPase

EntireName: KdpFABC P-type ATPase / Number of components: 1 / Oligomeric State: monomer
MassTheoretical: 154 kDa

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Component #1: protein, KdpA-subunit

ProteinName: KdpA-subunit / a.k.a: KdpA-subunit / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 59 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pGS4
Source (natural)Location in cell: membrane

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Component #2: protein, KdpB-subunit

ProteinName: KdpB-subunit / a.k.a: KdpB-subunit / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 72 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pGS4
Source (natural)Location in cell: membrane

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Component #3: protein, KdpC-subunit

ProteinName: KdpC-subunit / a.k.a: KdpC-subunit / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 21 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pGS4
Source (natural)Location in cell: membrane

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Component #4: protein, KdpF-subunit

ProteinName: KdpF-subunit / a.k.a: KdpF-subunit / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 3 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pGS4
Source (natural)Location in cell: membrane

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.005 mg/ml
Buffer solution: 50 mM MES pH 6.0, 50 mM NaCl, 5 mM MgCl2, 5 mM CaCl2
pH: 6
Support film400 mesh copper grid, carbon coated
Stainingapplied to freshly glow-discharged carbon-coated copper grids (400 mesh). Staining with 2 % (w/v) uranylacetic acid
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM120T / Date: Jul 20, 2004
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (nominal), 48000 X (calibrated) / Astigmatism: manually at 200000 on carbon film / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 432 - 864 nm
Specimen HolderHolder: room temperature holder / Model: SIDE ENTRY, EUCENTRIC / Temperature: 295 K ( 95 - 295 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 90 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10040
Details: started with angular reconstitution in IMAGIC (25 class averages) followed by projection matching in Spider (global search in 10 degree steps followed by local search in 2 degree steps)
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Sinogram Correlation followed by Projection Matching
Software: IMAGIC Spider / Resolution: 19 Å / Resolution method: FSC 0.5

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