+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8217 | |||||||||
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Title | MicroED structure of lysozyme at 1.8 A resolution | |||||||||
Map data | Lysozyme | |||||||||
Sample |
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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 | |||||||||
Biological species | Gallus gallus (chicken) / Chicken (chicken) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.8 Å | |||||||||
Authors | de la Cruz MJ / Hattne J / Shi D / Seidler P / Rodriguez J / Reyes FE / Sawaya MR / Cascio D / Eisenberg D / Gonen T | |||||||||
Citation | Journal: Nat Methods / Year: 2017 Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen / Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography. | |||||||||
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_8217.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-8217-v30.xml emd-8217.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_8217.png | 183.1 KB | ||
Filedesc structureFactors | emd_8217_sf.cif.gz | 910.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8217 | HTTPS FTP |
-Validation report
Summary document | emd_8217_validation.pdf.gz | 486.3 KB | Display | EMDB validaton report |
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Full document | emd_8217_full_validation.pdf.gz | 485.9 KB | Display | |
Data in XML | emd_8217_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_8217_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8217 | HTTPS FTP |
-Related structure data
Related structure data | 5k7oMC 8216C 8218C 8219C 8220C 8221C 8222C 8472C 5k7nC 5k7pC 5k7qC 5k7rC 5k7sC 5k7tC 5ty4C C: citing same article (ref.) M: atomic model generated by this map |
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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_8217.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Lysozyme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.59556 Å / Y: 0.59556 Å / Z: 0.58033 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: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 14.386 KDa |
-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: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 87 / 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
Concentration | 25 mg/mL | |||||||||
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Buffer | pH: 4.7 Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Digitization - Sampling interval: 0.0311999992 µm / Number grids imaged: 2 / Number real images: 1058 / Number diffraction images: 1058 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1500 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |