4QZB Transferase Dna date Jul 27, 2014
title Mouse Tdt In Complex With A Dsb Substrate, C-T Base Pair
authors J.Gouge, M.Delarue
compound source
Molecule: Dna Nucleotidylexotransferase
Chain: A
Fragment: See Remark 999
Synonym: Terminal Addition Enzyme, Terminal Deoxynucleotidyltransferase, Tdt, Terminal Transferase;
Ec: 2.7.7.31
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Dntt, Tdt
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Apapapapapc)-3'
Chain: D, U
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tptptptptpgpt)-3'
Chain: T
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.187 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.110 75.200 127.620 90.00 99.58 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand DCT, MG, NA enzyme Transferase E.C.2.7.7.31 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair., Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M, EMBO J. 2015 Apr 15;34(8):1126-42. doi: 10.15252/embj.201489643. Epub 2015 Mar, 11. PMID:25762590
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (4qzb.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 4QZB
  • CSU: Contacts of Structural Units for 4QZB
  • Structure Factors (734 Kb)
  • Retrieve 4QZB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QZB from S2C, [Save to disk]
  • Re-refined 4qzb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4QZB 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 4QZB
  • 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 4QZB, from MSDmotif at EBI
  • Fold representative 4qzb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qzb] [4qzb_D] [4qzb_U] [4qzb_A] [4qzb_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4QZB: [POLXc ] by SMART
  • Other resources with information on 4QZB
  • Community annotation for 4QZB at PDBWiki (http://pdbwiki.org)

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