3DIR

Crystallization of the Thermotoga maritima lysine riboswitch bound to N6-1-iminoethyl-L-Lysine

  • 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: 0.211
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 3DIR

Classification: RNA

Total Structure Weight: 57274.78

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

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

A N~6~-[(1Z)-ethanimidoyl]-L-lysine
C8 H17 N3 O2
ONYFNWIHJBLQKE-ZETCQYMHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-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 2 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
A NON-POLYMER C10 H16 N5 O14 P3 G
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: 0.211
  • R-Value Work: 0.178
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 54.81 α = 90.00
b = 78.84 β = 90.00
c = 143.32 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