2GQ4

Crystal structure of an RNA racemate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The first crystal structure of an RNA racemate.

Rypniewski, W.Vallazza, M.Perbandt, M.Klussmann, S.Delucas, L.J.Betzel, C.Erdmann, V.A.

(2006) Acta Crystallogr.,Sect.D 62: 659-664

  • DOI: 10.1107/S090744490601359X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The racemate of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) from Thermus flavus 5S rRNA has been crystallized and examined by X-ray crystallography. The space group is P1(_) with approximate unit-cell parameters a = 26.5, b = 38.0, c = 45.4 Angstrom, alph ...

    The racemate of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) from Thermus flavus 5S rRNA has been crystallized and examined by X-ray crystallography. The space group is P1(_) with approximate unit-cell parameters a = 26.5, b = 38.0, c = 45.4 Angstrom, alpha = 113.1, beta = 100.5, gamma = 93.3 degrees. The structure was solved by molecular replacement. There are four RNA duplexes in the unit cell. The crystal lattice consists of columns of RNA duplexes. The duplexes are stacked end-to-end and are stabilized by intermolecular base-stacking interactions. Within each column the L-duplexes and D-duplexes are stacked alternately. Every other duplex in each stack has two alternative conformations, approximately equally occupied, corresponding to molecules oriented in opposite directions. Neighbouring columns are related by the crystallographic centre of symmetry. The unit cell also contains approximately 250 ordered water molecules and six ordered calcium ions. A glycerol molecule is visible in the minor groove interacting with a guanosine residue.


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')K,M8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')L,N8N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
N
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
L, M, N
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
0G
Query on 0G
K, L, M, N
L-RNA LINKINGC10 H14 N5 O8 P

--

0C
Query on 0C
K, L, M, N
L-RNA LINKINGC9 H14 N3 O8 P

--

0U
Query on 0U
K, L, M, N
L-RNA LINKINGC9 H13 N2 O9 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.270 
  • Space Group: P -1
Unit Cell:
Length (Å)Angle (°)
a = 26.933α = 112.25
b = 38.160β = 101.56
c = 45.897γ = 92.20
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-03-28
    Type: Other