2GQ4

Crystal structure of an RNA racemate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.270 
  • R-Value Observed: 0.241 

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 D Biol Crystallogr 62: 659-664

  • DOI: 10.1107/S090744490601359X
  • Primary Citation of Related Structures:  
    2G32, 2GPM, 2GQ4, 2GQ5, 2GQ6, 2GQ7

  • 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, alpha = 113 ...

    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

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')A [auth K],
C [auth M]
8N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')B [auth L],
D [auth N]
8N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.270 
  • R-Value Observed: 0.241 
  • Space Group: P -1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.933α = 112.25
b = 38.16β = 101.56
c = 45.897γ = 92.2
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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