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 
  • R-Value Observed: 0.068 

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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 D Biol Crystallogr 69: 1530-1539

  • DOI: https://doi.org/10.1107/S0907444913010664
  • Primary Citation of Related Structures:  
    4HP2

  • 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 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   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiostrepton
A, B
19Streptomyces azureusMutation(s): 1 
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ETZ
Query on ETZ

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
P [auth B]
diethyl ether
C4 H10 O
RTZKZFJDLAIYFH-UHFFFAOYSA-N
DMF
Query on DMF

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
J [auth A]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
BB9
Query on BB9
A, B
PEPTIDE LINKINGC3 H5 N O2 SCYS
DBU
Query on DBU
A, B
PEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
A, B
PEPTIDE LINKINGC3 H5 N O2SER
MH6
Query on MH6
A, B
PEPTIDE LINKINGC3 H5 N O3SER
TS9
Query on TS9
A, B
L-PEPTIDE LINKINGC6 H13 N O4ILE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.64 Å
  • R-Value Work: 0.068 
  • R-Value Observed: 0.068 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 21.394α = 90
b = 22.87β = 106.45
c = 22.78γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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