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- EMDB-9292: MicroED structure of thiostrepton at 1.9 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-9292
TitleMicroED structure of thiostrepton at 1.9 A resolution
Map data2Fo-Fc map of thiostrepton
Sample
  • Organelle or cellular component: Thiostrepton
    • Protein or peptide: Thiostrepton
  • Ligand: water
KeywordsANTIBIOTIC
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / Thiostrepton
Function and homology information
Biological speciesStreptomyces azureus (bacteria)
Methodelectron crystallography / cryo EM / Resolution: 1.91 Å
AuthorsJones CG / Martynowycz MW
Funding support United States, 5 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1650604 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080269 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128936 United States
CitationJournal: ACS Cent Sci / Year: 2018
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
DepositionOct 30, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseNov 21, 2018-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.317655
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.317655
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mxf
  • Surface level: 0.317655
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mxf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9292.png

Downloads & links

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Map

FileDownload / File: emd_9292.map.gz / Format: CCP4 / Size: 363.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2Fo-Fc map of thiostrepton
Voxel sizeX: 0.59589 Å / Y: 0.59589 Å / Z: 0.68834 Å
Density
Contour LevelBy AUTHOR: 0.317655 / Movie #1: 0.317655
Minimum - Maximum-0.51279247 - 1.3747505
Average (Standard dev.)-0.0016757987 (±0.21176545)
SymmetrySpace group: 96
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-6-10-25
Dimensions564636
Spacing444440
CellA: 26.219 Å / B: 26.219 Å / C: 27.5336 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.595886363636360.595886363636360.68835
M x/y/z444440
origin x/y/z0.0000.0000.000
length x/y/z26.21926.21927.534
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S213
start NC/NR/NS-10-6-25
NC/NR/NS465636
D min/max/mean-0.5131.375-0.002

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Supplemental data

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Sample components

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Entire : Thiostrepton

EntireName: Thiostrepton
Components
  • Organelle or cellular component: Thiostrepton
    • Protein or peptide: Thiostrepton
  • Ligand: water

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Supramolecule #1: Thiostrepton

SupramoleculeName: Thiostrepton / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces azureus (bacteria)
Molecular weightTheoretical: 1.619538 KDa

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Macromolecule #1: Thiostrepton

MacromoleculeName: Thiostrepton / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces azureus (bacteria)
Molecular weightTheoretical: 1.805985 KDa
SequenceString:
(QUA)IA(DHA)AS(BB9)T(DBU)(DCY) (TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2)

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

BufferpH: 7 / Details: Powder
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 298 K / Details: Hand-plunged.
DetailsPowder
Crystal formationDetails: Powder

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 960 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Crystallography statisticsNumber intensities measured: 5578 / Number structure factors: 686 / Fourier space coverage: 78.6 / R sym: 0.236 / R merge: 0.236 / Overall phase error: 26.93 / Overall phase residual: 26.93 / Phase error rejection criteria: 0 / High resolution: 1.91 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.91 Å / Shell - Low resolution: 2.13 Å / Shell - Number structure factors: 92 / Shell - Phase residual: 29.19 / Shell - Fourier space coverage: 40.3 / Shell - Multiplicity: 4.9
Molecular replacementSoftware - Name: MOLREP (ver. 11.6.04)
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.11.14)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.91 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Merging software listSoftware - Name: AIMLESS (ver. 0.7.3)
DetailsFEI Ceta

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Atomic model buiding 1

Initial modelPDB ID:

1e9w


Chain - Chain ID: A / Chain - Residue range: 0-18 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 2.6
Output model

PDB-6mxf:
MicroED structure of thiostrepton at 1.9 A resolution

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