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- EMDB-1470: Molecular structure of the ParM polymer and the mechanism leading... -

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Basic information

Entry
Database: EMDB / ID: 1470
TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability
KeywordsGTPase / molecular switch / filament / ParM
SampleParM filament
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataA volume file of ParM filament
Methodhelical reconstruction, at 23 A resolution
AuthorsPopp D / Narita A / Oda T / Fujisawa T / Matsuo H / Nitanai Y / Iwasa M / Maeda K / Onishi H / Maeda Y
CitationEMBO J., 2008, 27, 570-579

EMBO J., 2008, 27, 570-579 StrPapers
Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability.
David Popp / Akihiro Narita / Toshiro Oda / Tetsuro Fujisawa / Hiroshi Matsuo / Yasushi Nitanai / Mitsusada Iwasa / Kayo Maeda / Hirofumi Onishi / Yuichiro Maéda

DateDeposition: Feb 14, 2008 / Header (metadata) release: Feb 19, 2008 / Map release: Mar 31, 2009 / Last update: Feb 14, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.0672E-5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9.0672E-5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1470.map.gz (map file in CCP4 format, 264 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
42 pix
4.01 A/pix
= 168.462 A
40 pix
4.01 A/pix
= 160.44 A
40 pix
4.01 A/pix
= 160.44 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.011 A
Density
Contour Level:0.00012, 9.07E-5 (movie #1):
Minimum - Maximum-6.98964e-05 - 0.000182333
Average (Standard dev.)6.82298e-06 (4.5134e-05)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions404042
Origin000
Limit393941
Spacing404042
CellA: 160.44 A / B: 160.44 A / C: 168.462 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.0114.0114.011
M x/y/z404042
origin x/y/z0.0000.0000.000
length x/y/z160.440160.440168.462
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404042
D min/max/mean-0.0000.0000.000

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Supplemental data

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Sample components

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Entire ParM filament

EntireName: ParM filament / Number of components: 1 / Oligomeric State: Filament
MassTheoretical: 35 kDa

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Component #1: protein, ParM

ProteinName: ParM / a.k.a: ParM / Oligomeric Details: Helical filament / Recombinant expression: Yes / Number of Copies: 10
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED
Sample solutionSpecimen conc.: 0.14 mg/ml
Buffer solution: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP
pH: 7.5
Staining1.0 % uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010HC
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 7 / Sampling size: 7 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: EOS / CTF correction: Each filament / Resolution: 23 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: situs / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD
Input PDB model: 1MWM
Chain ID: 1MWM_A
Output model

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