3B58 Rna date Oct 25, 2007
title Minimally Junctioned Hairpin Ribozyme Incorporates A38g Muta 2',5'-Phosphodiester Linkage At The Active Site
authors C.Macelrevey, J.Krucinska, J.E.Wedekind
compound source
Molecule: Loop A Substrate Strand
Chain: A
Engineered: Yes
Other_details: 2'5' Phosphodiester Linkage Between A6 And G
 Synthetic: Yes
Other_details: Solid-Phase Synthesis At Keck Institute, Yal

Molecule: 29-Mer Loop A And Loop B Ribozyme Strand
Chain: B
Engineered: Yes
Other_details: Synthetic Polyethylene Glycol Linker At Hing 14;
Synthetic: Yes
Other_details: Solid Phase Chemical Synthesis At Dharmacon, Colorado;

Molecule: Loop B S-Turn Strand
Chain: C
Engineered: Yes
Mutation: Yes
Synthetic: Yes
Other_details: Solid Phase Chemical Synthesis At Dharmacon,
symmetry Space Group: P 61 2 2
R_factor 0.236 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.370 93.370 132.270 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.65 Å
ligand NCO, S9L, SO4 enzyme
Primary referenceStructural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme., MacElrevey C, Salter JD, Krucinska J, Wedekind JE, RNA. 2008 Aug;14(8):1600-16. Epub 2008 Jul 2. PMID:18596253
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (3b58.pdb1.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 3B58
  • CSU: Contacts of Structural Units for 3B58
  • Likely Quarternary Molecular Structure file(s) for 3B58
  • Structure Factors (145 Kb)
  • Retrieve 3B58 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B58 from S2C, [Save to disk]
  • Re-refined 3b58 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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    • Visual 3D analysis of 3B58
  • 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 3B58, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b58] [3b58_A] [3b58_B] [3b58_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3B58
  • Community annotation for 3B58 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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