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- EMDB-2945: Structure of lysozyme solved by MicroED to 2.9 A -

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Basic information

Entry
Database: EMDB / ID: EMD-2945
TitleStructure of lysozyme solved by MicroED to 2.9 A
Map dataDiffraction data phased by molecular replacement (PDB ID: 3J4G)
Sample
  • Sample: Hen egg white lysozyme
  • Protein or peptide: Lysozyme C
Keywordslysozyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Methodelectron crystallography / cryo EM / Resolution: 2.9 Å
AuthorsShi D / Nannenga BL / Iadanza MG / Gonen T
CitationJournal: Elife / Year: 2013
Title: Three-dimensional electron crystallography of protein microcrystals.
Authors: Dan Shi / Brent L Nannenga / Matthew G Iadanza / Tamir Gonen /
Abstract: We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme ...We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1-1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name 'MicroED', that may have wide applicability in structural biology. DOI: http://dx.doi.org/10.7554/eLife.01345.001.
History
DepositionMar 18, 2015-
Header (metadata) releaseApr 1, 2015-
Map releaseApr 1, 2015-
UpdateApr 15, 2015-
Current statusApr 15, 2015Processing site: PDBe / 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-3j4g
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j4g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_2945.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDiffraction data phased by molecular replacement (PDB ID: 3J4G)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.71 Å/pix.
x 108 pix.
= 77.004 Å		0.71 Å/pix.
x 108 pix.
= 77.004 Å		0.69 Å/pix.
x 54 pix.
= 36.99 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.713 Å / Y: 0.713 Å / Z: 0.685 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-3.54059219 - 4.46073055
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 96
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-108-54-108
Dimensions10854108
Spacing10810854
CellA: 77.004 Å / B: 77.004 Å / C: 36.99 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.7130.7130.685
M x/y/z10810854
origin x/y/z0.0000.0000.000
length x/y/z77.00477.00436.990
α/β/γ90.00090.00090.000
start NX/NY/NZ-108-108-54
NX/NY/NZ10810854
MAP C/R/S321
start NC/NR/NS-54-108-108
NC/NR/NS54108108
D min/max/mean-3.5414.4610.000

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Supplemental data

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Sample components

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Entire : Hen egg white lysozyme

EntireName: Hen egg white lysozyme
Components
  • Sample: Hen egg white lysozyme
  • Protein or peptide: Lysozyme C

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Supramolecule #1000: Hen egg white lysozyme

SupramoleculeName: Hen egg white lysozyme / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 14.3 KDa

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Macromolecule #1: Lysozyme C

MacromoleculeName: Lysozyme C / type: protein_or_peptide / ID: 1 / Name.synonym: Hen egg white lysozyme / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: egg whites
Molecular weightTheoretical: 14.3 KDa
SequenceUniProtKB: Lysozyme C

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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

Concentration200 mg/mL
BufferpH: 4.5
Details: 3.5M sodium chloride; 15% PEG 5,000; 50 mM sodium acetate
GridDetails: glow discharged copper grid with holey carbon support
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: blot approximately 10 seconds before plunging
Detailsbatch crystallization
Crystal formationDetails: batch crystallization

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 110 K / Average: 100 K
Detailsselected area diffraction
DateJul 1, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2 / Camera length: 1500
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: -45 / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 45 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystal parametersUnit cell - A: 77 Å / Unit cell - B: 77 Å / Unit cell - C: 37 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 43 21 2

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