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 

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 D Biol Crystallogr 69: 1530-1539

  • DOI: 10.1107/S0907444913010664
  • Structures With Same Primary Citation

  • 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
ThiostreptonA, B19Streptomyces azureusMutation(s): 1 
Gene Names: tpdA
Find proteins for P0C8P8 (Streptomyces azureus)
Explore P0C8P8 
Go to UniProtKB:  P0C8P8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETZ
Query on ETZ

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

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, BTHIOSTREPTONT /  Antibiotic

--

Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
BB9
Query on BB9
A,BPEPTIDE LINKINGC3 H5 N O2 SCYS
DBU
Query on DBU
A,BPEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
A,BPEPTIDE LINKINGC3 H5 N O2SER
MH6
Query on MH6
A,BPEPTIDE LINKINGC3 H5 N O3SER
TS9
Query on TS9
A,BL-PEPTIDE LINKINGC6 H13 N O4ILE
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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