5HCH

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair.

Roethlisberger, P.Istrate, A.Marcaida Lopez, M.J.Visini, R.Stocker, A.Reymond, J.L.Leumann, C.J.

(2016) Chem.Commun.(Camb.) 52: 4749-4752

  • DOI: 10.1039/c6cc00374e

  • PubMed Abstract: 
  • DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties. Herein we report the first X-ray structure of a duplex containing a phen-pair in the ...

    DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties. Herein we report the first X-ray structure of a duplex containing a phen-pair in the center of the double helix in a zipper like stacking arrangement.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland. christian.leumann@dcb.unibe.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fucose-binding lectin
A
114Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: lecB
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HYN5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')B13synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')E13synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
61J
Query on 61J

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Download CCD File 
E
(6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol
C8 H17 O7 P
VFSMFEFBFABRKT-TVNFTVLESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
61H
Query on 61H
B, E
NON-POLYMERC19 H19 O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.227 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.451α = 90.00
b = 60.451β = 90.00
c = 204.828γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland20020_146646

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations