2ADW

Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.221 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Serendipitous Sad Phasing of an Echinomycin-(Acgtacgt)2 Bisintercalation Complex.

Cuesta-Seijo, J.A., Weiss, M.S., Sheldrick, G.M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 417

  • DOI: https://doi.org/10.1107/S0907444906003763
  • Primary Citation of Related Structures:  
    2ADW

  • PubMed Abstract: 

    • A new crystal form was obtained for the complex between (ACGTACGT)2 and echinomycin and X-ray data were collected to 1.6 A. The structure was phased by the SAD method based on a single unexpected anomalous scatterer that could be identified as a mixture of nickel and zinc by measurements of the anomalous scattering at different wavelengths ...

    A new crystal form was obtained for the complex between (ACGTACGT)2 and echinomycin and X-ray data were collected to 1.6 A. The structure was phased by the SAD method based on a single unexpected anomalous scatterer that could be identified as a mixture of nickel and zinc by measurements of the anomalous scattering at different wavelengths. This cation is coordinated by two guanines from two different duplexes and four water molecules. The structure resembles previously reported crystal structures of DNA-echinomycin complexes, except that three of the eight base pairs flanking the echinomycin bisintercalator sites have the Watson-Crick rather than the Hoogsteen configuration. Hoogsteen binding was found for the corresponding base pairs of the crystallographically independent duplex, indicating that the two configurations are very close in energy.

    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ECHINOMYCINE [auth H],
F [auth I],
G [auth J],
H [auth K]		8Streptomyces echinatusMutation(s): 2 
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'A,
B [auth C],
C [auth E],
D [auth G]		8N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
I [auth C]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
QUI
Query on QUI
Download Ideal Coordinates CCD File 
L [auth H],
M [auth H],
N [auth I],
O [auth I],
P [auth J],
L [auth H],
M [auth H],
N [auth I],
O [auth I],
P [auth J],
Q [auth J],
R [auth K],
S [auth K]
2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
K [auth E]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
NI
Query on NI
Download Ideal Coordinates CCD File 
J [auth E]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MVA
Query on MVA		E [auth H],
F [auth I],
G [auth J],
H [auth K]		L-PEPTIDE LINKINGC6 H13 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000491
Query on PRD_000491		E [auth H], F [auth I], G [auth J], H [auth K]EchinomycinCyclic depsipeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.221 
  • R-Value Observed: 0.180 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.904α = 90
b = 80.904β = 90
c = 48.194γ = 90
Software Package:
Software NamePurpose
SHELXDphasing
SHELXEmodel building
SHELXL-97refinement
HKL-2000data reduction
XDSdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    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