1DN5

SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN CRYSTALS GROWN AT TWO TEMPERATURES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures.

Chevrier, B.Dock, A.C.Hartmann, B.Leng, M.Moras, D.Thuong, M.T.Westhof, E.

(1986) J.Mol.Biol. 188: 707-719

  • Primary Citation of Related Structures:  1DN4

  • PubMed Abstract: 
  • Crystals of the hexadeoxyoligomer d(5BrC-G-5BrC-G-5BrC-G) were grown at different temperatures (5 degrees C, 18 degrees C and 37 degrees C) in the absence of divalent cations. The crystals grown at 5 degrees C did not diffract X-rays, while those gro ...

    Crystals of the hexadeoxyoligomer d(5BrC-G-5BrC-G-5BrC-G) were grown at different temperatures (5 degrees C, 18 degrees C and 37 degrees C) in the absence of divalent cations. The crystals grown at 5 degrees C did not diffract X-rays, while those grown at 18 degrees C and 37 degrees C did. The oligomer adopts the left-handed ZI conformation in both crystals. The main difference resides in a more extensive hydration shell in the crystal grown at high temperature than in the crystal grown at low temperature. The high-temperature crystal displays a spine of hydration running deep in the minor groove and linking exocyclic O-2 atoms of the pyrimidine rings. In both crystalline forms, a hydrated sodium ion bound to the N-7 of a guanine ring was found. Strings of water molecules bridging phosphate anionic oxygen atoms are found along the backbone. The absolute values of the propeller-twist are also different in both structures although the values of the twist are very similar. The results point to the importance of the crystallization conditions when analysing fine structural details like solvation properties of oligomers.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(CBR)P*GP*(CBR)P*GP*(CBR)P*G)-3')A,B6N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBR
Query on CBR
A, B
DNA LINKINGC9 H13 Br N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.930α = 90.00
b = 30.830β = 90.00
c = 44.730γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1987-04-16
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Experimental preparation