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Structure of hexameric DyP from Brevibacterium linens

by single particle reconstruction, at 16 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.18, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.18, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1530
TitleStructure of hexameric DyP from Brevibacterium linens
MapStructure of hexameric DyP from Brevibacterium linens
SampleStructure of hexameric DyP from Brevibacterium linens
Keywordsprotein complex, hexamer, peroxidase, dye-decolorizing peroxidase, heme containing peroxidase
AuthorsSutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N
DateDeposition: 2008-06-24, Header release: 2008-06-24, Map release: 2009-06-11, Last update: 2011-08-31
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.18, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.18, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 15, Issue 9, Page 939-47, Year 2008
TitleStructural basis of enzyme encapsulation into a bacterial nanocompartment.
AuthorsMarkus Sutter, Daniel Boehringer, Sascha Gutmann, Susanne Günther, David Prangishvili, Martin J Loessner, Karl O Stetter, Eilika Weber-Ban, Nenad Ban
ETH Zurich, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, 8093 Zurich, Switzerland.
KeywordsAmino Acid Sequence, Bacterial Proteins (chemistry), Binding Sites, Brevibacterium (enzymology), Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes (chemistry), Organelles (enzymology), Recombinant Proteins (chemistry), Sequence Homology, Amino Acid, Thermotoga maritima (enzymology)
LinksPubMed: 19172747, DOI: 10.1038/nsmb.1473
Map
Fileemd_1530.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.8 A/pix
= 179.2 A
64 pix
2.8 A/pix
= 179.2 A
64 pix
2.8 A/pix
= 179.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.1 (by author), 0.18 (movie #1):
Minimum - Maximum: -1.38813 - 0.944775
Average (Standard dev.): -0.00162246 (0.125636)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-31-32
Limit313231
Spacing646464
Unit CellA= B= C: 179.2 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.8 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.82.82.8
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS-31-32-32
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.3880.945-0.002
Annotation DetailsStructure of hexameric DyP from Brevibacterium linens
Supplement
Images
Images
Sample
NameStructure of hexameric DyP from Brevibacterium linens
Number of Components1
Oligomeric Statehexamer
Theoretical Mass0.24MDa
Detailsmonodisperse
Component #1: protein - Dyp
Scientific namedye-decolorizing peroxidase
Common NameDyp
Theoretical Mass0.04 MDa
Oligomeric Detailshexamer
Number of Copies6
Scientific Name of SpeciesBrevibacterium linens
NCBI taxonomy1703
StrainM18
Recombinant expressionYes
Engineered SourceVector: pET21a
Expression system: Escherichia coli Rosetta
LinksInter Pro: IPR:006314
Experiment
Sample Preparation
Staining2% w/v uranyl acetate
Specimen Support Detailscarbon coated 200 mesh copper grid
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 100000, Calibrated: 100000
Imaging ModeBRIGHT FIELD
Defocus700 nm - 1500 nm
Energy FilterEnergy Filter: Tridiem Gatan
Specimen Holder
HolderEucentric
ModelOTHER
Temperature295 K
Camera
DetectorGATAN ULTRASCAN 1000 (2k x 2k)
Image Acquisition
#1
Sampling Size1.4
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular reconstitution
SoftwareIMAGIC-5
CTF CorrectionEach image
Resolution By Author16 A
Resolution MethodFSC 3 sigma square root(6)
Single Particle
Number of Projections2878
Applied SymmetryD3 (2*3 fold dihedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1530.xml (6.9 KB)
Map dataemd_1530.map.gz (623.7 KB)
Images1530.gif (68.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1530
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.2 KB