[English] 日本語
Yorodumi
- EMDB-9292: MicroED structure of thiostrepton at 1.9 A resolution -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

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

emd_9292.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.69 Å/pix.
x 36 pix.
= 27.534 Å		0.6 Å/pix.
x 56 pix.
= 26.219 Å		0.6 Å/pix.
x 46 pix.
= 26.219 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.59589 Å / Y: 0.59589 Å / Z: 0.68834 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
Entire : Thiostrepton

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

-
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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

-
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

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
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
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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

DetailsFEI Ceta
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.91 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: MOLREP (ver. 11.6.04)
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.11.14)
Merging software listSoftware - Name: AIMLESS (ver. 0.7.3)
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more