5D4B 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, B
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: C, D, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tptptptptpgpg)-3')
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.730 71.450 198.170 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.66 Å
ligand MG, NA, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (5d4b.pdb1.gz) 127 Kb
  • Biological Unit Coordinates (5d4b.pdb2.gz) 126 Kb
  • LPC: Ligand-Protein Contacts for 5D4B
  • CSU: Contacts of Structural Units for 5D4B
  • Structure Factors (190 Kb)
  • Retrieve 5D4B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D4B from S2C, [Save to disk]
  • Re-refined 5d4b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D4B 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 5D4B
  • 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
  • Fold representative 5d4b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d4b_D] [5d4b_B] [5d4b_C] [5d4b_E] [5d4b_F] [5d4b] [5d4b_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D4B: [POLXc ] by SMART
  • Other resources with information on 5D4B
  • Community annotation for 5D4B at PDBWiki (http://pdbwiki.org)

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