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- EMDB-8608: Structure of E. coli MCE protein PqiB, periplasmic domain -

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Basic information

Entry
Database: EMDB / ID: 8608
TitleStructure of E. coli MCE protein PqiB, periplasmic domain
Samplehomo hexamer of PqiB
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataE. coli MCE protein PqiB, periplasmic domain
Methodsingle particle reconstruction, at 3.96 Å resolution
AuthorsBhabha G / Ekiert DC
CitationCell, 2017, 169, 273-285.e17

Cell, 2017, 169, 273-285.e17 StrPapers
Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale

DateDeposition: Feb 20, 2017 / Header (metadata) release: Apr 12, 2017 / Map release: Apr 12, 2017 / Last update: Feb 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5uvn
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8608.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.31 Å/pix.
= 262. Å
200 pix
1.31 Å/pix.
= 262. Å
200 pix
1.31 Å/pix.
= 262. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.055 (by author), 0.055 (movie #1):
Minimum - Maximum-0.18554376 - 0.40328574
Average (Standard dev.)0.0008848738 (0.010312201)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 262 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.311.311.31
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z262.000262.000262.000
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-0.1860.4030.001

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Supplemental data

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Sample components

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Entire homo hexamer of PqiB

EntireName: homo hexamer of PqiB / Number of components: 2
MassTheoretical: 347 kDa

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Component #1: protein, homo hexamer of PqiB

ProteinName: homo hexamer of PqiB / Recombinant expression: No
MassTheoretical: 347 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Paraquat-inducible protein B

ProteinName: Paraquat-inducible protein B / Recombinant expression: No
MassTheoretical: 48.857043 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: K12

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20 mM Tris pH 8.0 and 150 mM NaCl / pH: 8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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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: 80 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: 80 e/A2 is total dose for 50 frames

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 36591
3D reconstructionSoftware: RELION / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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