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

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Basic information

Entry
Database: EMDB / ID: EMD-4186
TitleGlutamine synthetase I from Mycobacterium smegmatis
Map dataGlutamine synthetase I from Mycobacterium smegmatis
Sample
  • Complex: Glutamine Synthetase I
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsKirykowicz AM / Woodward JD
CitationJournal: To Be Published
Title: Glutamine synthetase I from Mycobacterium smegmatis
Authors: Kirykowicz AM / Woodward JD
History
DepositionNov 30, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseDec 5, 2018-
UpdateDec 5, 2018-
Current statusDec 5, 2018Processing site: PDBe / Status: Released

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4186.png

Downloads & links

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Map

FileDownload / File: emd_4186.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlutamine synthetase I from Mycobacterium smegmatis
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.6 / Movie #1: 4.6
Minimum - Maximum-3.536475 - 8.174894
Average (Standard dev.)-0.000000001206191 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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
Components
  • Complex: Glutamine Synthetase I

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Supramolecule #1: Glutamine Synthetase I

SupramoleculeName: Glutamine Synthetase I / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Molecular weightExperimental: 648 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCl, 200 mM NaCl
StainingType: NEGATIVE / Material: Uranyl Acetate / Details: Sample washed/stained with 2% UA and air-dried
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
DetailsObtained from partially purified fraction

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 152 / Average exposure time: 0.5 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.2 mm / Nominal magnification: 50000
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2068 / Details: Manual picking
CTF correctionDetails: Ace2
Startup modelType of model: OTHER / Details: EMAN Common Lines used with C6 symmetry imposed
Final reconstructionNumber classes used: 68 / Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Details: EMAN procedure / Number images used: 2068
Initial angle assignmentType: COMMON LINE / Details: EMAN
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 68
Projection matching processing - Angular sampling: 5.0 degrees
Details: EMAN
Final 3D classificationNumber classes: 68

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