3GS1 Rna date Mar 26, 2009
title An All-Rna Hairpin Ribozyme With Mutation A38n1da
authors R.C.Spitale, R.Volpini, M.G.Heller, J.Krucinska, G.Cristalli, J.E.Wedekind
compound source
Molecule: Rna (5'- R(Upcpcpcpapgpupcpcpapcpcpgpu)-3');
Chain: A
Engineered: Yes
 Synthetic: Yes
Other_details: The Sequence Occurs Naturally In The Negative Polarity Strand Of The Tobacco Rinsgpot Virus Satellite Rna;

Molecule: Rna (5'-R(Cpgpgpupgpapgpapapgpgpg)- 3');
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Rna (5'- R(Pgpgpcpapgpapgpapapapcpapcpapcpgpa)-3');
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Rna (5'- R(Upcpgpupgpgpupapcpapupupapcpcpupgpcpc) -3');
Chain: D
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 61 2 2
R_factor 0.212 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.790 93.790 130.080 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.85 Å
ligand NCO, S9L, SO4 enzyme
Primary referenceIdentification of an Imino Group Indispensable for Cleavage by a Small Ribozyme., Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE, J Am Chem Soc. 2009 Apr 8. PMID:19354216
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (3gs1.pdb1.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 3GS1
  • CSU: Contacts of Structural Units for 3GS1
  • Likely Quarternary Molecular Structure file(s) for 3GS1
  • Structure Factors (83 Kb)
  • Retrieve 3GS1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GS1 from S2C, [Save to disk]
  • Re-refined 3gs1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3GS1 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3GS1
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3GS1, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gs1_B] [3gs1_C] [3gs1_D] [3gs1_A] [3gs1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3GS1
  • Community annotation for 3GS1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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