3DIM

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Cs+ 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: 2.9 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 3DIM

Classification: RNA

Total Structure Weight: 57691.82

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

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1PE
Query on 1PE

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

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

A CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPA
Query on IPA

A ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A 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
A RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.203
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 54.25 α = 90.00
b = 79.04 β = 90.00
c = 141.98 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: Advisory, Version format compliance