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Phosphoenolpyruvate synthase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)

by single particle reconstruction, at 29 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.5, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3.5, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5045
TitlePhosphoenolpyruvate synthase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
MapPhosphoenolpyruvate synthase structure from Desulfovibrio vulgaris Hildenborough (DvH)
SamplePhosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough
KeywordsPhosphoenolpyruvate synthase, Desulfovibrio vulgaris, DvH, PEP
AuthorsHan 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
DateDeposition: 2009-01-09, Header release: 2009-01-21, Map release: 2009-09-04, Last update: 2009-10-30
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.5, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3.5, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 39, Page 16580-5, Year 2009
TitleSurvey of large protein complexes in D. vulgaris reveals great structural diversity.
AuthorsBong-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
Life Sciences, Genomics, Earth Sciences, and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
KeywordsBacterial Proteins (chemistry), Crystallography, X-Ray, Databases, Protein, Desulfovibrio vulgaris (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Protein Conformation
LinksDOI: 10.1073/pnas.0813068106, PubMed: 19805340, PMC: PMC2742403
Map
Fileemd_5045.map.gz ( map file in CCP4 format, 2001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
4.23 A/pix
= 338.4 A
80 pix
4.23 A/pix
= 338.4 A
80 pix
4.23 A/pix
= 338.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3.4 (by author), 3.5 (movie #1):
Minimum - Maximum: -3.74918 - 23.0346
Average (Standard dev.): 4.8916e-10 (0.999999)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
Unit CellA= B= C: 338.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.23 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.74923.0350.000
Annotation DetailsPhosphoenolpyruvate synthase structure from Desulfovibrio vulgaris Hildenborough (DvH)
Supplement
Images
Images
Sample
NamePhosphoenolpyruvate synthase from Desulfovibrio vulgaris Hildenborough
Number of Components1
Oligomeric StateDimer
Theoretical Mass0.26MDa
Experimental Mass0.26MDa
Component #1: protein - Phosphoenolpyruvate synthase
Scientific namePhosphoenolpyruvate synthase
Theoretical Mass0.26 MDa
Experimental Mass0.26 MDa
Oligomeric DetailsDimer
Scientific Name of SpeciesDesulfovibrio vulgaris
Common Name of SpeciesDesulfovibrio vulgaris
NCBI taxonomy881
Recombinant expressionNo
Natural SourceCell: Desulfovibrio vulgaris Hildenborough
Cell Location: cytoplasmic
Experiment
Sample Preparation
StainingThree microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.
Specimen Conc0.015 mg/ml
Specimen Support Detailscarbon-coated and glow-discharged 300 mesh copper grid
Specimen Stateparticle
BufferDetails: 10 mM HEPES buffer
pH: 7
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 4000EX
Date03-APR-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage400 kV
Electron Dose17 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 30000, Calibrated: 30000
Astigmatismobjective lens astigmatism was corrected at 60,000 times magnification
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus600 nm - 2000 nm
Specimen Holder
HolderSide entry room T
ModelOTHER
Tilt Angle0 degrees - 50 degrees
Temperature293 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images11
Sampling Size6.35
Quant Bit Number8
DetailsThe images were scanned with a resolution of 6.35 micro m per pixel and later averaged 2 fold in each direction.
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmRandom conical tilt (RCT)
SoftwareSPIDER
CTF CorrectionEach particle
Resolution By Author29 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections2105
Applied SymmetryC2 (2 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-5045.xml (7.9 KB)
Map dataemd_5045.map.gz (1.7 MB)
Imagesemd_5045_1.jpg (34.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5045
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.3 KB