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- EMDB-1637: Proteome organization in a genome-reduced bacterium -Topoisomeras... -

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Basic information

Entry
Database: EMDB / ID: 1637
TitleProteome organization in a genome-reduced bacterium -Topoisomerase of Mycoplasma pneumoniae -
KeywordsTopoisomerase / Mycoplasma pneumoniae / single particle
SampleTopoisomerase from Mycoplasma pneumoniae
SourceMycoplasma pneumoniae / bacteria / マイコプラズマ・ニューモニアエ, 肺炎マイコプラズマ
Map dataMap of topoisomerase
Methodsingle particle reconstruction, at 21.5 A resolution
AuthorsKuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P / Castano-Diez D / Chen W-H / Devos D / Guell Cargol M / Norambuena T / Racke I / Rybin V / Schmidt A / Yus E / Aebersold R / Herrmann R / Bottcher B / Frangakis AS / Russell RB / Serrano L / Bork P / Gavin A-C
CitationScience, 2009, 326, 1235-1240

Science, 2009, 326, 1235-1240 StrPapers
Proteome organization in a genome-reduced bacterium.
Sebastian Kühner / Vera van Noort / Matthew J Betts / Alejandra Leo-Macias / Claire Batisse / Michaela Rode / Takuji Yamada / Tobias Maier / Samuel Bader / Pedro Beltran-Alvarez / Daniel Castaño-Diez / Wei-Hua Chen / Damien Devos / Marc Güell / Tomas Norambuena / Ines Racke / Vladimir Rybin / Alexander Schmidt / Eva Yus / Ruedi Aebersold / Richard Herrmann / Bettina Böttcher / Achilleas S Frangakis / Robert B Russell / Luis Serrano / Peer Bork / Anne-Claude Gavin

DateDeposition: Aug 3, 2009 / Header (metadata) release: Jun 11, 2010 / Map release: Jun 11, 2010 / Last update: Aug 3, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1637.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5.2 A/pix
= 332.8 A
64 pix
5.2 A/pix
= 332.8 A
64 pix
5.2 A/pix
= 332.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.2 A
Density
Contour Level:6 (by author), 6 (movie #1):
Minimum - Maximum0 - 72.1255
Average (Standard dev.)0.291584 (2.90852)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 332.8 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z5.25.25.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean0.00072.1250.292

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Supplemental data

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Sample components

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Entire Topoisomerase from Mycoplasma pneumoniae

EntireName: Topoisomerase from Mycoplasma pneumoniae / Details: Sample was fixed following the GRAFIX protocol / Number of components: 1

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Component #1: protein, Topoisomerase

ProteinName: Topoisomerase / a.k.a: Topoisomerase / Recombinant expression: Yes
SourceSpecies: Mycoplasma pneumoniae / bacteria / マイコプラズマ・ニューモニアエ, 肺炎マイコプラズマ
Source (engineered)Expression System: Mycoplasma pneumoniae / bacteria / マイコプラズマ・ニューモニアエ, 肺炎マイコプラズマ

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50mM Hepes, 20% glycerol, 0.075% glutaraldehyde, 100mM NaCl, 1.5 mM MgCl2
pH: 7.5
Support film400 mesh copper grid
StainingGrids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece of carbon, which was also floated on 1% uranyl acetate, was picked up with the same grid sandwiching the sample between the two layers of carbon
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 27500 X (nominal)
Astigmatism: Corrected at 200000 times magnification on graininess of carbon
Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: GENERIC CCD

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Image acquisition

Image acquisitionNumber of digital images: 70 / Sampling size: 14.22 microns / Bit depth: 12
Details: Images were recorded on CCD, no scanning sampling step size was adjusted to calibrated image size

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 4767 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: IMAGIC, SPIDER, EMAN
Details: Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space
Resolution: 21.5 A / Resolution method: FSC 0.5

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