1E9W | pdb_00001e9w

Structure of the macrocycle thiostrepton solved using the anomalous dispersive contribution from sulfur

• PDB DOI: https://doi.org/10.2210/pdb1E9W/pdb

• Classification: ANTIBIOTIC
• Organism(s): Streptomyces azureus
• Mutation(s): No 


• Deposited: 2000-10-27 Released: 2001-03-23 
• Deposition Author(s): Bond, C.S., Shaw, M.P., Alphey, M.S., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.142 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.118 (DCC) 
• R-Value Observed: 
  0.112 (Depositor) 

Starting Model: other

Literature

Structure of the Macrocycle Thiostrepton Solved Using the Anomalous Dispersive Contribution from Sulfur

Bond, C.S., Shaw, M.P., Alphey, M.S., Hunter, W.N.

(2001) Acta Crystallogr D Biol Crystallogr 57: 755

• PubMed: 11320328 
• DOI: https://doi.org/10.1107/s0907444901003134
• Primary Citation Related Structures: 
  1E9W


• PubMed Abstract: 
  

  The structure of a tetragonal crystal form of thiostrepton has been solved using the anomalous dispersive effects of five S atoms from high-redundancy data collected to 1.33 A resolution at the Cu Kalpha wavelength. Data measured to 1.02 A resolution with a synchrotron source were used for refinement. Details of the molecular structure, intramolecular and intermolecular interactions are given.

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Organizational Affiliation: 
• The Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1.81 kDa 
• Atom Count: 118 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THIOSTREPTON	A	19	Streptomyces azureus	Mutation(s): 0
UniProt
Find proteins for P0C8P8 (Streptomyces azureus) Explore P0C8P8  Go to UniProtKB:  P0C8P8

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BB9	A	PEPTIDE LINKING	C3 H5 N O2 S		CYS
DBU	A	PEPTIDE LINKING	C4 H7 N O2		THR
DCY	A	D-PEPTIDE LINKING	C3 H7 N O2 S		--
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER
MH6	A	PEPTIDE LINKING	C3 H5 N O3		SER
TS9	A	L-PEPTIDE LINKING	C6 H13 N O4		ILE

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000223	A	THIOSTREPTON	Thiopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.142 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.118 (DCC) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.577	α = 90
b = 26.577	β = 90
c = 27.436	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-23 
Deposition Author(s): Bond, C.S., Shaw, M.P., Alphey, M.S., Hunter, W.N.

Revision History  

• Version 1.0: 2001-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 2.0: 2019-04-24
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2019-05-22
  Changes: Data collection, Refinement description
• Version 2.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description