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- EMDB-10090: Hen egg-white lysozyme by serial electron diffraction -

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Basic information

Entry
Database: EMDB / ID: EMD-10090
TitleHen egg-white lysozyme by serial electron diffraction
Map data
Sample
  • Complex: Lysozyme
    • Protein or peptide: Lysozyme C
  • Ligand: water
Keywordslysozyme / HEWL / serial crystallography / HYDROLASE
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: 1.8 Å
AuthorsBuecker R / Mehrabi P
CitationJournal: Nat Commun / Year: 2020
Title: Serial protein crystallography in an electron microscope.
Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / ...Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / R J Dwayne Miller /
Abstract: Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample ...Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
History
DepositionJun 21, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s2n
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10090.png

Downloads & links

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Map

FileDownload / File: emd_10090.map.gz / Format: CCP4 / Size: 5.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.4 Å/pix.
x 134 pix.
= 53.041 Å		0.44 Å/pix.
x 102 pix.
= 44.823 Å		0.44 Å/pix.
x 111 pix.
= 48.778 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.43944 Å / Y: 0.43944 Å / Z: 0.39583 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.569848 - 8.900104000000001
Average (Standard dev.)0.03304088 (±0.46641004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-55-20
Dimensions102111134
Spacing111102134
CellA: 48.77784 Å / B: 44.82288 Å / C: 53.04122 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.439441441441440.439441176470590.39582835820896
M x/y/z111102134
origin x/y/z0.0000.0000.000
length x/y/z48.77844.82353.041
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-55-1-20
NC/NR/NS111102134
D min/max/mean-2.5708.9000.033

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Supplemental data

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Sample components

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Entire : Lysozyme

EntireName: Lysozyme
Components
  • Complex: Lysozyme
    • Protein or peptide: Lysozyme C
  • Ligand: water

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Supramolecule #1: Lysozyme

SupramoleculeName: Lysozyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Lysozyme C

MacromoleculeName: Lysozyme C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 14.33116 KDa
SequenceString:
KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDIT ASVNCAKKIV SDGNGMNAWV AWRNRCKGTD VQAWIRGCRL

UniProtKB: Lysozyme C

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 60 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: OTHER / Number grids imaged: 1 / Average exposure time: 0.006 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 5.0 µm / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Camera length: 1570 mm
Sample stageTilt angle: 0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber intensities measured: 16139 / Number structure factors: 9444 / Fourier space coverage: 80.8 / R sym: 0.23 / R merge: 0.23 / Overall phase error: 29.4 / Overall phase residual: 1 / Phase error rejection criteria: 0 / High resolution: 1.8 Å
Details: Data reduction/reconstruction using X-ray crystallographic software (CrystFEL, Phaser, cctbx.refine, Coot)
Shell - Shell ID: 1 / Shell - High resolution: 30.0 Å / Shell - Low resolution: 0.1 Å / Shell - Number structure factors: 1 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 1 / Shell - Multiplicity: 1

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