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- EMDB-6314: Catalase solved at 3.2 Angstrom resolution by MicroED -

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Basic information

Entry
Database: EMDB / ID: EMD-6314
TitleCatalase solved at 3.2 Angstrom resolution by MicroED
Map dataCatalase diffraction data phased by molecular replacement
Sample
  • Sample: catalase
  • Protein or peptide: catalase
Keywordscatalase / microcrystal
Function / homology
Function and homology information


catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
Methodelectron crystallography / cryo EM / Resolution: 3.2 Å
AuthorsNannenga BL / Shi D / Hattne J / Reyes FE / Gonen T
CitationJournal: Elife / Year: 2014
Title: Structure of catalase determined by MicroED.
Authors: Brent L Nannenga / Dan Shi / Johan Hattne / Francis E Reyes / Tamir Gonen /
Abstract: MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of ...MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.
History
DepositionMar 31, 2015-
Header (metadata) releaseApr 8, 2015-
Map releaseApr 8, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j7b
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6314.gif

Downloads & links

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Map

FileDownload / File: emd_6314.map.gz / Format: CCP4 / Size: 17.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCatalase diffraction data phased by molecular replacement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.75 Å/pix.
x 90 pix.
= 67.64 Å		0.8 Å/pix.
x 216 pix.
= 172.081 Å		0.76 Å/pix.
x 240 pix.
= 182.071 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.75156 Å / Y: 0.79667 Å / Z: 0.75863 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-3.71510458 - 5.38364077
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 19
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions21624090
Spacing21690240
CellA: 67.64004 Å / B: 172.08072 Å / C: 182.0712 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.751555555555560.79667129629630.75862916666667
M x/y/z90216240
origin x/y/z0.0000.0000.000
length x/y/z67.640172.081182.071
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ90216240
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS24021690
D min/max/mean-3.7155.384-0.000

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Supplemental data

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Sample components

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Entire : catalase

EntireName: catalase
Components
  • Sample: catalase
  • Protein or peptide: catalase

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Supramolecule #1000: catalase

SupramoleculeName: catalase / type: sample / ID: 1000 / Details: catalase microcrystals / Oligomeric state: tetramer / Number unique components: 1
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: catalase

MacromoleculeName: catalase / type: protein_or_peptide / ID: 1 / Details: catalase microcrystals / Oligomeric state: tetramer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: liver
Molecular weightTheoretical: 240 KDa
SequenceUniProtKB: Catalase

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 6.3 / Details: 50 mM sodium phosphate
GridDetails: 300 mesh copper grid with holey carbon support
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV
Method: Crystals were added to the grid for 30 seconds and then blotted for 2 to 6 seconds.
DetailsCatalase containing 10% sodium chloride was dialyzed overnight in 50 mM sodium phosphate to remove the sodium chloride. Crystals formed following dialysis.
Crystal formationDetails: Catalase containing 10% sodium chloride was dialyzed overnight in 50 mM sodium phosphate to remove the sodium chloride. Crystals formed following dialysis.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 110 K / Average: 100 K
DateJun 15, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2 / Camera length: 2000
Details: Raw diffraction images are available upon request. Contact the Gonen lab for access.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: -55 / Tilt angle max: 55 / Tilt series - Axis1 - Min angle: -55 ° / Tilt series - Axis1 - Max angle: 55 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystal parametersUnit cell - A: 67.84 Å / Unit cell - B: 172.08 Å / Unit cell - C: 182.070 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 21 21 21

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