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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9292 | ||||||||||||||||||
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Title | MicroED structure of thiostrepton at 1.9 A resolution | ||||||||||||||||||
![]() | 2Fo-Fc map of thiostrepton | ||||||||||||||||||
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![]() | ANTIBIOTIC | ||||||||||||||||||
Function / homology | Thiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / Thiostrepton![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | electron crystallography / cryo EM / Resolution: 1.91 Å | ||||||||||||||||||
![]() | Jones CG / Martynowycz MW | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination. Authors: Christopher G Jones / Michael W Martynowycz / Johan Hattne / Tyler J Fulton / Brian M Stoltz / Jose A Rodriguez / Hosea M Nelson / Tamir Gonen / ![]() Abstract: In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful ...In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule's structure requires X-ray and/or neutron diffraction studies. In practice, however, X-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the electron cryo-microscopy (cryoEM) method microcrystal electron diffraction (MicroED) to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high-quality MicroED data from nanocrystals (∼100 nm, ∼10 g) resulting in atomic resolution (<1 Å) crystal structures in minutes. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 255.9 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
Images | ![]() | 177.2 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Filedesc structureFactors | ![]() | 20.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 489.8 KB | Display | ![]() |
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Full document | ![]() | 489.4 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mxfMC ![]() 9282C ![]() 9283C ![]() 9284C ![]() 9285C ![]() 9286C ![]() 9287C ![]() 9288C ![]() 9289C ![]() 9290C ![]() 9291C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 2Fo-Fc map of thiostrepton | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.59589 Å / Y: 0.59589 Å / Z: 0.68834 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Thiostrepton
Entire | Name: Thiostrepton |
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Components |
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-Supramolecule #1: Thiostrepton
Supramolecule | Name: Thiostrepton / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.619538 KDa |
-Macromolecule #1: Thiostrepton
Macromolecule | Name: Thiostrepton / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.805985 KDa |
Sequence | String: (QUA)IA(DHA)AS(BB9)T(DBU)(DCY) (TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2) |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 2 / 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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![]() | electron crystallography |
Aggregation state | 3D array |
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Sample preparation
Buffer | pH: 7 / Details: Powder |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 298 K / Details: Hand-plunged. |
Details | Powder |
Crystal formation | Details: Powder |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number diffraction images: 214 / Average exposure time: 2.21 sec. / Average electron dose: 0.09 e/Å2 / Details: FEI CetaD |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 960 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |