6MXF

MicroED structure of thiostrepton at 1.9 A resolution


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.91 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination.

Jones, C.G.Martynowycz, M.W.Hattne, J.Fulton, T.J.Stoltz, B.M.Rodriguez, J.A.Nelson, H.M.Gonen, T.

(2018) ACS Cent Sci 4: 1587-1592

  • DOI: https://doi.org/10.1021/acscentsci.8b00760
  • Primary Citation of Related Structures:  
    6MXF

  • PubMed 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 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 -15 g) resulting in atomic resolution (<1 Å) crystal structures in minutes.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, Departments of Biological Chemistry and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiostrepton19Streptomyces azureusMutation(s): 0 
UniProt
Find proteins for P0C8P8 (Streptomyces azureus)
Explore P0C8P8 
Go to UniProtKB:  P0C8P8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C8P8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
BB9
Query on BB9
A
PEPTIDE LINKINGC3 H5 N O2 SCYS
DBU
Query on DBU
A
PEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
A
PEPTIDE LINKINGC3 H5 N O2SER
MH6
Query on MH6
A
PEPTIDE LINKINGC3 H5 N O3SER
TS9
Query on TS9
A
L-PEPTIDE LINKINGC6 H13 N O4ILE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.91 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.219α = 90
b = 26.219β = 90
c = 27.534γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0232

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1650604
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM080269
Department of Energy (DOE, United States)United StatesDE-FC02-02ER63421
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128867
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128936

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-02
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 2.0: 2019-11-27
    Changes: Author supporting evidence, Polymer sequence
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2023-11-15
    Changes: Data collection, Derived calculations