3DIO

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, IRIDIUM HEXAMINE SOAK

  • Classification: RNA
  • Deposited: 2008-06-20 Released: 2008-09-16
  • Deposition author(s): Serganov, A.A.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 3DIO

Classification: RNA

Total Structure Weight: 62092.43

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (174-MER) X 174 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IRI
Query on IRI

X IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1PE
Query on 1PE

X PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LYS
Query on LYS

X LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

X POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

X SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CCC
Query on CCC
X RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.204
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 53.92 α = 90.00
b = 78.00 β = 90.00
c = 140.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-20
  • Released Date: 2008-09-16
  • Deposition author(s): Serganov, A.A.

Revision History

  • Version 1_0: 2008-09-16

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance