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- EMDB-10736: Lumazine Synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-10736
TitleLumazine Synthase
Map dataReconstruction of Lumazine Synthase, sharpened and filtered at 2 angstroms
Sample
  • Complex: Icosahedral complex of Lumazine Synthase
Biological speciesAquifex aeolicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsBhella D / Streetley J / Clarke M / Cowton V / Patel A / Bammes B / Hosogi N
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12014/7 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17135 United Kingdom
CitationJournal: Biophys Rev / Year: 2019
Title: Cryo-electron microscopy: an introduction to the technique, and considerations when working to establish a national facility.
Authors: David Bhella /
History
DepositionMar 9, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10736.png

Downloads & links

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Map

FileDownload / File: emd_10736.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Lumazine Synthase, sharpened and filtered at 2 angstroms
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.6 Å/pix.
x 400 pix.
= 238.8 Å		0.6 Å/pix.
x 400 pix.
= 238.8 Å		0.6 Å/pix.
x 400 pix.
= 238.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.597 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05662378 - 0.0998149
Average (Standard dev.)-0.00012479199 (±0.007047362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 238.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5970.5970.597
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z238.800238.800238.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0570.100-0.000

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Supplemental data

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Mask #1

Fileemd_10736_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_10736_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_10736_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Icosahedral complex of Lumazine Synthase

EntireName: Icosahedral complex of Lumazine Synthase
Components
  • Complex: Icosahedral complex of Lumazine Synthase

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Supramolecule #1: Icosahedral complex of Lumazine Synthase

SupramoleculeName: Icosahedral complex of Lumazine Synthase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Aquifex aeolicus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.2
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsPurified by immobilised metal affinity chromatography.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 13.0 µm / Digitization - Frames/image: 1-41 / Number grids imaged: 1 / Number real images: 1199 / Average exposure time: 10.0 sec. / Average electron dose: 1.66 e/Å2
Details: Images were acquired at 141 FPS with 2 x binning and electron counting. A total of 41 summed frames were written out.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 200000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 198385 / Details: Automated particle picking in Relion
CTF correctionSoftware - Name: RELION (ver. 3.1b) / Software - details: with GCTF
Startup modelType of model: OTHER / Details: SGD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1b) / Number images used: 16258
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1b)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1b)
FSC plot (resolution estimation)

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