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- EMDB-1678: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -

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Basic information

Entry
Database: EMDB / ID: 1678
TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
KeywordsAAA+ atpase / metallation / tetrapyrroles
SampleComplex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
SourceRhodobacter capsulatus / archaea / ロドバクター・カプスラータス
Map dataCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
Methodsingle particle reconstruction, at 14 A resolution
AuthorsLundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S
CitationStructure, 2010, 18, 354-365

Structure, 2010, 18, 354-365 StrPapers
ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
Joakim Lundqvist / Hans Elmlund / Ragna Peterson Wulff / Lisa Berglund / Dominika Elmlund / Cecilia Emanuelsson / Hans Hebert / Robert D Willows / Mats Hansson / Martin Lindahl / Salam Al-Karadaghi

DateDeposition: Jan 8, 2010 / Header (metadata) release: Jan 18, 2010 / Map release: Jan 21, 2010 / Last update: Jan 8, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1678.map.gz (map file in CCP4 format, 2001 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
2.33 A/pix
= 186.4 A
80 pix
2.33 A/pix
= 186.4 A
80 pix
2.33 A/pix
= 186.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.33 A
Density
Contour Level:0.005 (by author), 0.005 (movie #1):
Minimum - Maximum-0.0280966 - 0.0773895
Average (Standard dev.)0.000822421 (0.00452024)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
CellA=B=C: 186.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.332.332.33
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z186.400186.400186.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.0280.0770.001

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Supplemental data

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Sample components

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Entire Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP

EntireName: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
Number of components: 1
MassTheoretical: 660 kDa

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Component #1: protein, Biosynthetic enzyme

ProteinName: Biosynthetic enzyme / a.k.a: Mg chelatase / Recombinant expression: Yes
MassTheoretical: 660 kDa
SourceSpecies: Rhodobacter capsulatus / archaea / ロドバクター・カプスラータス
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 stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 8
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
LensMagnification: 60000 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: JEOL

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Image acquisition

Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 526 / Number of projections: 17623 / Applied symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 14 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1G8P
Output model

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