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Proteome organization in a genome-reduced bacterium -Topoisomerase of Mycoplasma pneumoniae -

by single particle reconstruction, at 21.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 6, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 6, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1637
TitleProteome organization in a genome-reduced bacterium -Topoisomerase of Mycoplasma pneumoniae -
MapMap of topoisomerase
SampleTopoisomerase from Mycoplasma pneumoniae
KeywordsTopoisomerase, Mycoplasma pneumoniae, single particle
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
DateDeposition: 2009-08-03, Header release: 2010-06-11, Map release: 2010-06-11, Last update: 2010-06-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 6, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 6, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleScience, Vol. 326, Issue 5957, Page 1235-40, Year 2009
TitleProteome organization in a genome-reduced bacterium.
AuthorsSebastian 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
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
KeywordsBacterial Proteins (analysis), Computational Biology, Genome, Bacterial, Mass Spectrometry (methods), Metabolic Networks and Pathways, Microscopy, Electron, Models, Biological, Models, Molecular, Multiprotein Complexes (analysis), Mycoplasma pneumoniae (chemistry), Pattern Recognition, Automated, Protein Interaction Mapping, Proteome, Systems Biology
LinksDOI: 10.1126/science.1176343, PubMed: 19965468
Map
Fileemd_1637.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:6 (by author), 6 (movie #1):
Minimum - Maximum: 0 - 72.1255
Average (Standard dev.): 0.291584 (2.90852)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
Unit CellA= B= C: 332.8 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5.2 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean0.00072.1250.292
Annotation DetailsMap of topoisomerase
Supplement
Images
Images
Sample
NameTopoisomerase from Mycoplasma pneumoniae
Number of Components1
DetailsSample was fixed following the GRAFIX protocol
Component #1: protein - Topoisomerase
Scientific nameTopoisomerase
Scientific Name of SpeciesMycoplasma pneumoniae
NCBI taxonomy2104
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 2104
Expression system: Mycoplasma pneumoniae
Experiment
Sample Preparation
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
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 50mM Hepes, 20% glycerol, 0.075% glutaraldehyde, 100mM NaCl, 1.5 mM MgCl2
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 27500
AstigmatismCorrected at 200000 times magnification on graininess of carbon
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorGENERIC CCD
Image Acquisition
#1
Number of Digital Images70
Sampling Size14.22
Quant Bit Number12
DetailsImages were recorded on CCD, no scanning sampling step size was adjusted to calibrated image size
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareIMAGIC, SPIDER, EMAN
DetailsSpider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space
Resolution By Author21.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections4767
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1637.xml (7.3 KB)
Map dataemd_1637.map.gz (19.5 KB)
Images1637.png (200.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1637
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.3 KB