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PDBsum entry 2gpm

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ligands metals links
RNA PDB id
2gpm
Jmol
Contents
Ligands
_0C-_0U-_0G-_0G-
_0G-_0C-_0G-_0G
×2
_0C-_0C-_0G-_0C-
_0C-_0U-_0G-_0G
×2
Metals
_CA ×6
Waters ×281
PDB id:
2gpm
Name: RNA
Title: Crystal structure of an RNA racemate
Structure: RNA (5'-r( (0C)p (0U)p (0G)p (0G)p (0G)p (0C)p (0 3'). Chain: k, m. Engineered: yes. RNA (5'-r( (0C)p (0C)p (0G)p (0C)p (0C)p (0U)p (0 3'). Chain: l, n. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence is a 'spiegelmer' and occurs i from thermus flavus. From thermus flavus
Biol. unit: Dimer (from PQS)
Resolution:
1.40Å     R-factor:   0.241     R-free:   0.270
Ensemble: 2 models
Authors: W.Rypniewski,M.Vallazza,M.Perbandt,S.Klussmann,C.Betzel,V.A.
Key ref:
W.Rypniewski et al. (2006). The first crystal structure of an RNA racemate. Acta Crystallogr D Biol Crystallogr, 62, 659-664. PubMed id: 16699193 DOI: 10.1107/S090744490601359X
Date:
18-Apr-06     Release date:   27-Jun-06    
 Headers
 References

 

 
DOI no: 10.1107/S090744490601359X Acta Crystallogr D Biol Crystallogr 62:659-664 (2006)
PubMed id: 16699193  
 
 
The first crystal structure of an RNA racemate.
W.Rypniewski, M.Vallazza, M.Perbandt, S.Klussmann, L.J.Delucas, C.Betzel, V.A.Erdmann.
 
  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 = 113.1, 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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 A hydrated calcium ion capping the terminal sugar moiety of G86. The contours correspond to the 2F[o] - F[c] electron density at one r.m.s. level. Water molecules are labelled W.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 659-664) copyright 2006.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20530536 A.Eichert, K.Behling, C.Betzel, V.A.Erdmann, J.P.Fürste, and C.Förster (2010).
The crystal structure of an 'All Locked' nucleic acid duplex.
  Nucleic Acids Res, 38, 6729-6736.
PDB code: 2x2q
  19193994 A.Eichert, A.Schreiber, J.P.Fürste, M.Perbandt, C.Betzel, V.A.Erdmann, and C.Förster (2009).
Escherichia coli tRNA(Arg) acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 98.  
  19153458 A.Eichert, M.Perbandt, A.Schreiber, J.P.Fürste, C.Betzel, V.A.Erdmann, and C.Förster (2009).
X-ray diffraction analysis of a human tRNA(Gly) acceptor-stem microhelix isoacceptor at 1.18 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 59-62.  
18658118 W.Rypniewski, D.A.Adamiak, J.Milecki, and R.W.Adamiak (2008).
Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.
  RNA, 14, 1845-1851.
PDB codes: 3czw 3d0m
  17909284 C.Förster, A.B.Brauer, D.Lehmann, T.Borowski, S.Brode, J.P.Fürste, M.Perbandt, C.Betzel, and V.A.Erdmann (2007).
Cocrystallizing natural RNA with its unnatural mirror image: biochemical and preliminary X-ray diffraction analysis of a 5S rRNA A-helix racemate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 839-843.  
  17909289 C.Förster, K.Szkaradkiewicz, M.Perbandt, A.B.Brauer, T.Borowski, J.P.Fürste, C.Betzel, and V.A.Erdmann (2007).
Human tRNA(Gly) acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 858-861.  
  17183173 C.Förster, M.Perbandt, A.B.Brauer, S.Brode, J.P.Fürste, C.Betzel, and V.A.Erdmann (2007).
Crystallization and preliminary X-ray diffraction analysis of an Escherichia coli tRNA(Gly) acceptor-stem microhelix.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 46-48.  
17555763 D.Lambert, and D.E.Draper (2007).
Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions.
  J Mol Biol, 370, 993.  
17389378 M.D.Smith, and R.A.Collins (2007).
Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme.
  Proc Natl Acad Sci U S A, 104, 5818-5823.  
17288535 M.Egli, and P.S.Pallan (2007).
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
  Annu Rev Biophys Biomol Struct, 36, 281-305.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.