5DI2 Rna date Aug 31, 2015
title Two Divalent Metal Ions And Conformational Changes Play Role Hammerhead Ribozyme Cleavage Reaction-Wt Ribozyme In Mn2+ A
authors A.Mir, J.Chen, D.Neau, B.L.Golden
compound source
Molecule: Rna (48-Mer)
Chain: A
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Artificially Evolved Hammerhead Ribozyme-Rzb

Molecule: 5'-R(Gpgpgpcpgpu)-D(Pc)- R(Pupgpgpgpcpapgpupapcpcpcpa)-3';
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemical Synthesis
symmetry Space Group: C 2 2 21
R_factor 0.221 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.625 85.815 103.753 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.99 Å
ligand MN enzyme
Primary referenceTwo Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction., Mir A, Chen J, Robinson K, Lendy E, Goodman J, Neau D, Golden BL, Biochemistry. 2015 Oct 2. PMID:26398724
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (5di2.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 5DI2
  • CSU: Contacts of Structural Units for 5DI2
  • Structure Factors (180 Kb)
  • Retrieve 5DI2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DI2 from S2C, [Save to disk]
  • Re-refined 5di2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DI2 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 5DI2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5di2_B] [5di2_A] [5di2]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5DI2
  • Community annotation for 5DI2 at PDBWiki (http://pdbwiki.org)

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