5D49 Transferase date Aug 07, 2015
title Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recomb
authors J.Loc'H, S.Rosario, M.Delarue
compound source
Molecule: Terminal Deoxynucleotidyltransferase
Chain: A
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Dntt
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Dna (5'-D(Apapapapapc)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tptptptptpgpgpc)-3')
Chain: C, D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Apapapapa)-3')
Chain: E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.197 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.550 74.250 126.150 90.00 101.84 90.00
method X-Ray Diffractionresolution 1.99 Å
ligand ACT, MG, NA, PG4, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination., Loc'h J, Rosario S, Delarue M, Structure. 2016 Sep 6;24(9):1452-1463. doi: 10.1016/j.str.2016.06.014. Epub 2016 , Aug 4. PMID:27499438
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (5d49.pdb1.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 5D49
  • CSU: Contacts of Structural Units for 5D49
  • Structure Factors (284 Kb)
  • Retrieve 5D49 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D49 from S2C, [Save to disk]
  • Re-refined 5d49 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D49 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 5D49
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d49_C] [5d49_D] [5d49] [5d49_E] [5d49_B] [5d49_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D49: [POLXc ] by SMART
    • Other resources with information on 5D49
  • Community annotation for 5D49 at PDBWiki (http://pdbwiki.org)

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