2DVI Transferase Rna date Jul 31, 2006
title Complex Structure Of Cca-Adding Enzyme, Mini-Dcc And Ctp
authors K.Tomita, R.Ishitani, S.Fukai, O.Nureki
compound source
Molecule: Trna (34-Mer)
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Cca-Adding Enzyme
Chain: A
Synonym: Trna Nucleotidyltransferase, Trna Adenylyl- Cytidylyl-Transferase, Trna Cca-Pyrophosphorylase, Trna- Nt;
Engineered: Yes

Organism_scientific: Archaeoglobus Fulgidus
Organism_taxid: 2234
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 43 21 2
R_factor 0.207 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
58.004 58.004 431.498 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.61 Å
ligand CTP, MG, SO4 enzyme Transferase E.C. BRENDA

Primary referenceComplete crystallographic analysis of the dynamics of CCA sequence addition., Tomita K, Ishitani R, Fukai S, Nureki O, Nature. 2006 Oct 26;443(7114):956-60. Epub 2006 Oct 15. PMID:17051158
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (2dvi.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 2DVI
  • CSU: Contacts of Structural Units for 2DVI
  • Likely Quarternary Molecular Structure file(s) for 2DVI
  • Structure Factors (185 Kb)
  • Retrieve 2DVI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DVI from S2C, [Save to disk]
  • Re-refined 2dvi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DVI 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 2DVI
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2DVI, from MSDmotif at EBI
  • Fold representative 2dvi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dvi] [2dvi_A] [2dvi_B]
  • SWISS-PROT database: [O28126]
  • Domain organization of [CCA_ARCFU] by SWISSPFAM
  • Other resources with information on 2DVI
  • Community annotation for 2DVI 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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