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Yorodumi- EMDB-0864: MicroED structure of lysozyme at 1.73A determained using crystal ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0864 | |||||||||||||||
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Title | MicroED structure of lysozyme at 1.73A determained using crystal lamellas prepared by focused ion beam milling | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information 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 Gram-positive bacterium / defense response to bacterium ...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 Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Gallus gallu (chicken) / Chicken (chicken) | |||||||||||||||
Method | electron crystallography / cryo EM / Resolution: 1.73 Å | |||||||||||||||
Authors | Zhou H / Luo Z / Li X | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: J Struct Biol / Year: 2019 Title: Using focus ion beam to prepare crystal lamella for electron diffraction. Authors: Heng Zhou / Zhipu Luo / Xueming Li / Abstract: Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the ...Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0864.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-0864-v30.xml emd-0864.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_0864.png | 173.1 KB | ||
Filedesc structureFactors | emd_0864_sf.cif.gz | 293.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0864 | HTTPS FTP |
-Related structure data
Related structure data | 6lavMC 0865C 6lawC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0864.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X: 0.56419 Å / Y: 0.56419 Å / Z: 0.59202 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : lysozyme
Entire | Name: lysozyme |
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Components |
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-Supramolecule #1: lysozyme
Supramolecule | Name: lysozyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Gallus gallu (chicken) |
-Macromolecule #1: Lysozyme C
Macromolecule | Name: Lysozyme C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme |
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Source (natural) | Organism: Chicken (chicken) |
Molecular weight | Theoretical: 14.33116 KDa |
Sequence | String: KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDIT ASVNCAKKIV SDGNGMNAWV AWRNRCKGTD VQAWIRGCRL |
-Macromolecule #2: ACETATE ION
Macromolecule | Name: ACETATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ACT |
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Molecular weight | Theoretical: 59.044 Da |
Chemical component information | ChemComp-ACT: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 37 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 4.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1200 mm |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 0.057 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Crystal parameters | Unit cell - A: 78.99 Å / Unit cell - B: 78.99 Å / Unit cell - C: 37.89 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 43 21 2 |
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Crystallography statistics | Number intensities measured: 121300 / Number structure factors: 11548 / Fourier space coverage: 89 / R sym: 0.281 / R merge: 0.281 / Overall phase error: 0 / Overall phase residual: 1 / Phase error rejection criteria: 60 / High resolution: 1.7 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.7 Å / Shell - Low resolution: 1.76 Å / Shell - Number structure factors: 1002 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 79.1 / Shell - Multiplicity: 9.7 |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.73 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6lav: |