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- EMDB-23957: MicroED structure of lysozyme from milled crystals at 1.75A -

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Basic information

Entry
Database: EMDB / ID: EMD-23957
TitleMicroED structure of lysozyme from milled crystals at 1.75A
Map data2mFo-Fc map wrapped around protein with 3A carve
Sample
  • Complex: Lysozyme
    • Protein or peptide: Lysozyme C
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsLysozyme / 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 / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive 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: 1.75 Å
AuthorsMartynowycz MW / Gonen T
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
CitationJournal: To be Published
Title: Preparing crystalline lamellae by focused ion-beam milling for microcrystal electron diffraction (MicroED) experiments
Authors: Martynowycz MW / Gonen T
History
DepositionMay 7, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_23957.png

Downloads & links

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Map

FileDownload / File: emd_23957.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2mFo-Fc map wrapped around protein with 3A carve
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.39 Å/pix.
x 123 pix.
= 48.521 Å		0.43 Å/pix.
x 99 pix.
= 42.691 Å		0.43 Å/pix.
x 101 pix.
= 43.553 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.43122 Å / Y: 0.43122 Å / Z: 0.39448 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.1363873 - 7.147704
Average (Standard dev.)0.040977463 (±0.52904975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-97-50-62
Dimensions99101123
Spacing10199123
CellA: 43.55322 Å / B: 42.69078 Å / C: 48.521038 Å
α=β=γ: 90.0 °

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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: SODIUM ION
  • Ligand: CHLORIDE ION
  • 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)
Molecular weightTheoretical: 14.3 KDa

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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: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 78 / 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 state3D array

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Sample preparation

Concentration20 mg/mL
BufferpH: 4.7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS TALOS
TemperatureMin: 77.0 K / Max: 85.0 K
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1500 / Number diffraction images: 1500 / Average exposure time: 1.0 sec. / Average electron dose: 0.01 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus min: 0.0 µm / Camera length: 2100 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN / Tilt angle: -30.0, 30.0

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Image processing

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.75 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber intensities measured: 305349 / Number structure factors: 12144 / Fourier space coverage: 100 / R merge: 0.23 / Overall phase error: 18 / Overall phase residual: 19 / Phase error rejection criteria: none / High resolution: 1.75 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.75 Å / Shell - Low resolution: 34.18 Å / Shell - Number structure factors: 12144 / Shell - Phase residual: 18 / Shell - Fourier space coverage: 100 / Shell - Multiplicity: 25

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Atomic model buiding 1

Initial modelPDB ID:

5k7o


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 25 / Target criteria: LL
Output model

PDB-7mrp:
MicroED structure of lysozyme from milled crystals at 1.75A

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