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- EMDB-5045: Phosphoenolpyruvate synthase structure : Structural survey of lar... -

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Basic information

Entry
Database: EMDB / ID: EMD-5045
TitlePhosphoenolpyruvate synthase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
Map dataPhosphoenolpyruvate synthase structure from Desulfovibrio vulgaris Hildenborough (DvH)
Sample
  • Sample: Phosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough
  • Protein or peptide: Phosphoenolpyruvate synthase
KeywordsPhosphoenolpyruvate synthase / Desulfovibrio vulgaris / DvH / PEP
Biological speciesDesulfovibrio vulgaris (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 29.0 Å
AuthorsHan B-G / Dong M / Liu H / Camp L / Geller J / Singer M / Hazen TC / Choi M / Witkowska HE / Ball DA ...Han B-G / Dong M / Liu H / Camp L / Geller J / Singer M / Hazen TC / Choi M / Witkowska HE / Ball DA / Typke D / Downing KH / Shatsky M / Brenner SE / Chandonia J-M / Biggin MD / Glaeser RM
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Survey of large protein complexes in D. vulgaris reveals great structural diversity.
Authors: Bong-Gyoon Han / Ming Dong / Haichuan Liu / Lauren Camp / Jil Geller / Mary Singer / Terry C Hazen / Megan Choi / H Ewa Witkowska / David A Ball / Dieter Typke / Kenneth H Downing / Maxim ...Authors: Bong-Gyoon Han / Ming Dong / Haichuan Liu / Lauren Camp / Jil Geller / Mary Singer / Terry C Hazen / Megan Choi / H Ewa Witkowska / David A Ball / Dieter Typke / Kenneth H Downing / Maxim Shatsky / Steven E Brenner / John-Marc Chandonia / Mark D Biggin / Robert M Glaeser /
Abstract: An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr approximately 400 k. The quaternary ...An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr approximately 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate approximately 10 times greater than that of previous "proteomic" screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.
History
DepositionJan 9, 2009-
Header (metadata) releaseJan 21, 2009-
Map releaseSep 4, 2009-
UpdateOct 30, 2009-
Current statusOct 30, 2009Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5045_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5045.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhosphoenolpyruvate synthase structure from Desulfovibrio vulgaris Hildenborough (DvH)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.23 Å/pix.
x 80 pix.
= 338.4 Å		4.23 Å/pix.
x 80 pix.
= 338.4 Å		4.23 Å/pix.
x 80 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.5
Minimum - Maximum-3.74918 - 23.034600000000001
Average (Standard dev.)0.00000000048916 (±0.999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 338.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.234.234.23
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z338.400338.400338.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-3.74923.0350.000

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Supplemental data

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Sample components

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Entire : Phosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough

EntireName: Phosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough
Components
  • Sample: Phosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough
  • Protein or peptide: Phosphoenolpyruvate synthase

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Supramolecule #1000: Phosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough

SupramoleculeName: Phosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough
type: sample / ID: 1000 / Oligomeric state: Dimer / Number unique components: 1
Molecular weightExperimental: 260 KDa / Theoretical: 260 KDa

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Macromolecule #1: Phosphoenolpyruvate synthase

MacromoleculeName: Phosphoenolpyruvate synthase / type: protein_or_peptide / ID: 1 / Name.synonym: Phosphoenolpyruvate synthase / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Desulfovibrio vulgaris (bacteria) / synonym: Desulfovibrio vulgaris / Cell: Desulfovibrio vulgaris Hildenborough / Location in cell: cytoplasmic
Molecular weightExperimental: 260 KDa / Theoretical: 260 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7 / Details: 10 mM HEPES buffer
StainingType: NEGATIVE
Details: Three microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.
GridDetails: carbon-coated and glow-discharged 300 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 4000EX
TemperatureAverage: 293 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
DateApr 3, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 11 / Average electron dose: 17 e/Å2
Details: The images were scanned with a resolution of 6.35 micro m per pixel and later averaged 2 fold in each direction.
Bits/pixel: 8
Tilt angle min0
Electron beamAcceleration voltage: 400 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 30000
Sample stageSpecimen holder: Side entry room T / Specimen holder model: OTHER / Tilt angle max: 50

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 2105

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