1XVK

X-ray structure of an Echinomycin-(GCGTACGC)2 complex

• PDB DOI: https://doi.org/10.2210/pdb1XVK/pdb
• NAKB: 1XVK

• Classification: DNA/ANTIBIOTIC
• Organism(s): Streptomyces echinatus
• Mutation(s): Yes 


• Deposited: 2004-10-28 Released: 2005-04-12 
• Deposition Author(s): Cuesta-Seijo, J.A., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.221 
• R-Value Observed: 0.183 

Literature

Structures of Complexes between Echinomycin and Duplex DNA.

Cuesta-Seijo, J.A., Sheldrick, G.M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 442

• PubMed: 15805599 
• DOI: https://doi.org/10.1107/S090744490500137X
• Primary Citation of Related Structures:  
  1PFE, 1XVK, 1XVN, 1XVR


• PubMed Abstract: 
  

  The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1-1.5 A) are reported for the complexes of echinomycin with (GCGTACGC)2 (at both low and high ionic strengths) and (ACGTACGT)2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson-Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis-intercalating antibiotics and the duplex DNA than were previously available.

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Organizational Affiliation: 

Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, D37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.61 kDa 
• Atom Count: 357 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHINOMYCIN	B	8	Streptomyces echinatus	Mutation(s): 2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'	A	8	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUI	D [auth B], E [auth B]	2-CARBOXYQUINOXALINE C9 H6 N2 O2 UPUZGXILYFKSGE-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000491	B	Echinomycin	Cyclic depsipeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.221 
• R-Value Observed: 0.183 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.183	α = 90
b = 39.183	β = 90
c = 79.89	γ = 120

Software Package:

Software Name	Purpose
EPMR	phasing
SHELXL-97	refinement
HKL-2000	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Cuesta-Seijo, J.A., Sheldrick, G.M.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other
• Version 1.5: 2020-09-09
  Changes: Advisory, Database references, Derived calculations, Structure summary