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- EMDB-6313: 2.5A structure of lysozyme solved by MicroED -

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Basic information

Entry
Database: EMDB / ID: EMD-6313
Title2.5A structure of lysozyme solved by MicroED
Map dataLysozyme electron diffraction phased by molecular replacement. PDB ID 3J6K.
Sample
  • Sample: Hen egg white lysozyme
  • Protein or peptide: Lysozyme C
Keywordslysozyme / microcrystal
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: 2.5 Å
AuthorsNannenga BL / Shi D / Leslie AGW / Gonen T
CitationJournal: Nat Methods / Year: 2014
Title: High-resolution structure determination by continuous-rotation data collection in MicroED.
Authors: Brent L Nannenga / Dan Shi / Andrew G W Leslie / Tamir Gonen /
Abstract: MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called 'continuous ...MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called 'continuous rotation'. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology.
History
DepositionMar 27, 2015-
Header (metadata) releaseApr 8, 2015-
Map releaseApr 8, 2015-
UpdateApr 8, 2015-
Current statusApr 8, 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-3j6k
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6k
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6313.gif

Downloads & links

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Map

FileDownload / File: emd_6313.map.gz / Format: CCP4 / Size: 3.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLysozyme electron diffraction phased by molecular replacement. PDB ID 3J6K.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.61 Å/pix.
x 125 pix.
= 75.96 Å		0.61 Å/pix.
x 125 pix.
= 75.96 Å		0.62 Å/pix.
x 60 pix.
= 37.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.60768 Å / Y: 0.60768 Å / Z: 0.62033 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-3.15723062 - 5.18146324
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 96
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-125-60-125
Dimensions12560125
Spacing12512560
CellA: 75.96 Å / B: 75.96 Å / C: 37.219982 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.607680.607680.62033333333333
M x/y/z12512560
origin x/y/z0.0000.0000.000
length x/y/z75.96075.96037.220
α/β/γ90.00090.00090.000
start NX/NY/NZ-125-125-60
NX/NY/NZ12512560
MAP C/R/S321
start NC/NR/NS-60-125-125
NC/NR/NS60125125
D min/max/mean-3.1575.1810.000

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Supplemental data

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Segmentation: This mask represents the map masked around the...

AnnotationThis mask represents the map masked around the asymmetric unit (PDB 3J6K)
Fileemd_6313_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 / Details: lysozyme microcrystals / Oligomeric state: 1 / 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: lysozyme / Details: lysozyme microcrystals / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: egg white
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: 50 mM sodium acetate, 3.5 M sodium chloride, 15% PEG5000
GridDetails: 300 mesh copper grid with holey carbon support
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV
Method: Add crystals to grid for 30 seconds and blot for 10-12 seconds.
Detailsbatch crystallization
Crystal formationDetails: batch crystallization

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 110 K / Average: 100 K
DateFeb 4, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2 / Camera length: 1500
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: -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: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystal parametersUnit cell - A: 75.96 Å / Unit cell - B: 75.96 Å / Unit cell - C: 37.22 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 43 21 2

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