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- EMDB-1680: Macromolecular crystal data phased by negative staining electron ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1680
TitleMacromolecular crystal data phased by negative staining electron microscopy reconstructions
Map dataMacromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle
Sample
  • Sample: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
  • Protein or peptide: CaDHQ
KeywordsNegative staining / electron microscopy / reconstructions / phasing
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsTrapani S / Schoehn G / Navaza J / Abergel C
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions.
Authors: Stefano Trapani / Guy Schoehn / Jorge Navaza / Chantal Abergel /
Abstract: The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing ...The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein.
History
DepositionJan 13, 2010-
Header (metadata) releaseJan 18, 2010-
Map releaseJan 28, 2011-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 165
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 165
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1680.map.gz / Format: CCP4 / Size: 2.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMacromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 87 pix.
= 121.8 Å
1.4 Å/pix.
x 87 pix.
= 121.8 Å
1.4 Å/pix.
x 87 pix.
= 121.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy EMDB: 165.0 / Movie #1: 165
Minimum - Maximum-335.0 - 426.47199999999998
Average (Standard dev.)31.211500000000001 (±113.128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions878787
Spacing878787
CellA=B=C: 121.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z878787
origin x/y/z0.0000.0000.000
length x/y/z121.800121.800121.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS878787
D min/max/mean-335.000426.47231.212

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Supplemental data

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Sample components

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Entire : Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)

EntireName: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
Components
  • Sample: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
  • Protein or peptide: CaDHQ

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Supramolecule #1000: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)

SupramoleculeName: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
type: sample / ID: 1000 / Oligomeric state: Dodecamer / Number unique components: 1
Molecular weightExperimental: 200 KDa

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Macromolecule #1: CaDHQ

MacromoleculeName: CaDHQ / type: protein_or_peptide / ID: 1 / Name.synonym: CaDHQ / Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 17 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.05 mg/mL
BufferpH: 7.4 / Details: 20mM NaCl, 10mM Tris-HCL
StainingType: NEGATIVE
Details: Negative staining using 1% methylamine vanadate, CH3NH2VO3
GridDetails: 400 mesk copper grid
VitrificationCryogen name: NONE / Instrument: OTHER / Details: Negative staining at room temperature

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Electron microscopy

MicroscopeJEOL 1200EXII
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DetailsLow dose negative staining
DateDec 12, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 8 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each negative
Final two d classificationNumber classes: 114
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider
Details: 7200 particles included in the reconstruction (out of 12000). 432 symmetry imposed
Number images used: 7200

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