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- EMDB-1677: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -

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Entry
Database: EMDB / ID: 1677
TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of ATP
KeywordsAAA+ atpase / metallation / tetrapyrroles
SampleComplex of Mg-chelatase subunits BchI and BchD in presence of ATP
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 ATP
Methodsingle particle reconstruction, at 13 Å 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 Yorodumi Papers
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

Validation ReportPDB-ID: 2x31

SummaryFull reportAbout validation report
DateDeposition: Jan 8, 2010 / Header (metadata) release: Jan 18, 2010 / Map release: Jan 21, 2010 / Last update: Mar 13, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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Map

Fileemd_1677.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
2.33 Å/pix.
= 186.4 Å
80 pix
2.33 Å/pix.
= 186.4 Å
80 pix
2.33 Å/pix.
= 186.4 Å

Surface

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.33 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.817642 - 1.62923
Average (Standard dev.)0.0217686 (0.146476)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
CellA=B=C: 186.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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-0.8181.6290.022

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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 ATP

EntireName: Complex of Mg-chelatase subunits BchI and BchD in presence of ATP
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
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: JEOL

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Image acquisition

Image acquisitionNumber of digital images: 15 / Scanner: ZEISS SCAI

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 616 / Number of projections: 30721 / Applied symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 13 Å / 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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