[English] 日本語
Yorodumi
- EMDB-1680: Macromolecular crystal data phased by negative staining electron ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1680
TitleMacromolecular crystal data phased by negative staining electron microscopy reconstructions
KeywordsNegative staining / electron microscopy / reconstructions / phasing
SampleType-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
SourceCandida albicans / yeast / カンジダ・アルビカンス
Map dataMacromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle
Methodsingle particle reconstruction, at 15 Å resolution
AuthorsTrapani S / Schoehn G / Navaza J / Abergel C
CitationActa Crystallogr. D Biol. Crystallogr., 2010, 66, 514-521

Acta Crystallogr. D Biol. Crystallogr., 2010, 66, 514-521 StrPapers
Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions.
Stefano Trapani / Guy Schoehn / Jorge Navaza / Chantal Abergel

DateDeposition: Jan 13, 2010 / Header (metadata) release: Jan 18, 2010 / Map release: Jan 28, 2011 / Last update: Jan 13, 2010

-
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
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_1680.map.gz (map file in CCP4 format, 2574 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:165 (by emdb), 165 (movie #1):
Minimum - Maximum-335 - 426.472
Average (Standard dev.)31.2115 (113.128)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions878787
Origin000
Limit868686
Spacing878787
CellA=B=C: 121.8 Å
α=β=γ: 90 deg.

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

-
Supplemental data

-
Sample components

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

EntireName: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
Number of components: 1 / Oligomeric State: Dodecamer
MassExperimental: 200 kDa

-
Component #1: protein, CaDHQ

ProteinName: CaDHQ / a.k.a: CaDHQ / Oligomeric Details: Dodecamer / Recombinant expression: Yes / Number of Copies: 12
MassTheoretical: 17 kDa
SourceSpecies: Candida albicans / yeast / カンジダ・アルビカンス
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.05 mg/ml / Buffer solution: 20mM NaCl, 10mM Tris-HCL / pH: 7.4
Support film400 mesk copper grid
StainingNegative staining using 1% methylamine vanadate, CH3NH2VO3
VitrificationInstrument: NONE / Cryogen name: NONE / Details: Negative staining at room temperature

-
Electron microscopy imaging

ImagingMicroscope: JEOL 1200EXII / Date: Dec 12, 2006 / Details: Low dose negative staining
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: OTHER
LensMagnification: 50000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderHolder: Eucentric / Model: JEOL
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 8 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

-
Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 114 / Number of projections: 7200 / Applied symmetry: T (tetrahedral)
3D reconstructionAlgorithm: Back projection / Software: Spider / CTF correction: Each negative
Details: 7200 particles included in the reconstruction (out of 12000). 432 symmetry imposed
Resolution: 15 Å / Resolution method: FSC 0.5

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more