4HP2

Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.64 Å
  • R-Value Work: 0.068 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 angstrom resolution.

Propper, K.Holstein, J.J.Hubschle, C.B.Bond, C.S.Dittrich, B.

(2013) Acta Crystallogr.,Sect.D 69: 1530-1539

  • DOI: 10.1107/S0907444913010664

  • PubMed Abstract: 
  • A new monoclinic solvate containing two molecules of the thiopeptide antibiotic thiostrepton in the asymmetric unit has been crystallized in space group P2(1). Single-crystal diffraction data to a resolution of 0.64 Å were collected at the SLS synchr ...

    A new monoclinic solvate containing two molecules of the thiopeptide antibiotic thiostrepton in the asymmetric unit has been crystallized in space group P2(1). Single-crystal diffraction data to a resolution of 0.64 Å were collected at the SLS synchrotron, allowing structure solution by direct methods and resolution of the disorder present. Valence electron density can be observed in the Fourier residual density from refinement with the independent-atom model, which is a prerequisite for successful application of more sophisticated aspherical-atom scattering factors such as the invariom model when aiming to improve the structural model. Invariom refinement improves quality indicators such as R1(F) for thiostrepton, as previously demonstrated for small molecules. The nonspherical electron-density model also allows the direct derivation of a dipole moment and an electrostatic potential for the whole molecule, which is discussed in the context of antibiotic activity and molecular recognition.


    Organizational Affiliation

    Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiostrepton
A, B
19Streptomyces azureusMutation(s): 0 
Gene Names: tpdA
Find proteins for P0C8P8 (Streptomyces azureus)
Go to UniProtKB:  P0C8P8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETZ
Query on ETZ

Download SDF File 
Download CCD File 
A, B
diethyl ether
C4 H10 O
RTZKZFJDLAIYFH-UHFFFAOYSA-N
 Ligand Interaction
DMF
Query on DMF

Download SDF File 
Download CCD File 
A, B
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000223
Query on PRD_000223
A,BTHIOSTREPTONThiopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.64 Å
  • R-Value Work: 0.068 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 21.394α = 90.00
b = 22.870β = 106.45
c = 22.780γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description
  • Version 1.2: 2018-04-04
    Type: Data collection