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;
Ec: 2.7.7.25, 2.7.7.21
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
crystal
cell
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.2.7.7.25 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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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