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- EMDB-4186: Glutamine synthetase I from Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: 4186
TitleGlutamine synthetase I from Mycobacterium smegmatis
Map dataGlutamine synthetase I from Mycobacterium smegmatis
SampleGlutamine Synthetase I:
SourceMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / negative staining / 24 Å resolution
AuthorsKirykowicz AM / Woodward JD
CitationJournal: To Be Published
Title: Glutamine synthetase I from Mycobacterium smegmatis
Authors: Kirykowicz AM / Woodward JD
DateDeposition: Nov 30, 2017 / Header (metadata) release: Dec 13, 2017 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4186.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5.4 Å/pix.
= 345.6 Å
64 pix
5.4 Å/pix.
= 345.6 Å
64 pix
5.4 Å/pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.4 Å
Density
Contour Level:4.6 (by author), 4.6 (movie #1):
Minimum - Maximum-3.536475 - 8.174894
Average (Standard dev.)-0.000000001206191 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32.0-32.0-32.0
Limit31.031.031.0
Spacing646464
CellA=B=C: 345.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-3.5368.175-0.000

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Supplemental data

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Sample components

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Entire Glutamine Synthetase I

EntireName: Glutamine Synthetase I / Number of components: 1

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Component #1: protein, Glutamine Synthetase I

ProteinName: Glutamine Synthetase I / Recombinant expression: No
MassExperimental: 648 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.3 mg/ml / Buffer solution: 50 mM Tris-HCl, 200 mM NaCl / pH: 8
StainingSample washed/stained with 2% UA and air-dried
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: OTHER
LensMagnification: 50000.0 X (nominal) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 152

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D6 (2*6 fold dihedral) / Number of projections: 2068
3D reconstructionCTF correction: Ace2 / Resolution: 24 Å / Resolution method: FSC 0.5 CUT-OFF / Details: EMAN procedure / Euler angles: EMAN

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