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- EMDB-4916: Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.8 A... -

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Basic information

Entry
Database: EMDB / ID: EMD-4916
TitleCryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.8 Angstrom resolution
Map data
SampleCytochrome bd-I oxidase from E. coliUbiquinol oxidase (H+-transporting)
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsSafarian S / Hahn A / Kuehlbrandt W / Michel H
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 ? resolution
Authors: Safarian S / Hahn A / Kuehlbrandt S / Michel S
Validation ReportSummary, Full report, XML, About validation report
History
DepositionApr 30, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseJun 3, 2020-
UpdateJun 3, 2020-
Current statusJun 3, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4916.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å
0.83 Å/pix.
x 300 pix.
= 249.6 Å
0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.38385907 - 0.55066735
Average (Standard dev.)0.00017370153 (±0.009779043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3840.5510.000

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Supplemental data

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Sample components

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Entire Cytochrome bd-I oxidase from E. coli

EntireName: Cytochrome bd-I oxidase from E. coliUbiquinol oxidase (H+-transporting)
Number of components: 1

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Component #1: protein, Cytochrome bd-I oxidase from E. coli

ProteinName: Cytochrome bd-I oxidase from E. coliUbiquinol oxidase (H+-transporting)
Recombinant expression: No
MassTheoretical: 107.7 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pet17b_cydABX-StrepII / Strain: C43

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 7 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 96000 X (nominal), 96000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (70.0 - 70.0 K)
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5463

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 245000
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Cross-correlation coefficient / Refinement space: REAL / Overall bvalue: 120

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