3ECP Dna Recombination Dna date Sep 01, 2008
title Crystal Structure Of Tn5 Transposase Complexed With 5' Phosp Transposon End Dna
authors V.A.Klenchin
compound source
Molecule: Tn5 Transposase
Chain: A
Fragment: Tn5 Transposase
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Orf163
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_plasmid: Ptyb1

Molecule: Dna Transferred Strand
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Transposase Recognition Sequence Occurs Natu The Tn5 Transposon;

Molecule: Dna Non-Transferred Strand
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Transposase Recognition Sequence Occurs Natu The Tn5 Transposon
symmetry Space Group: P 65 2 2
R_factor 0.219 R_Free 0.274
length a length b length c angle alpha angle beta angle gamma
113.508 113.508 228.775 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand GOL enzyme
  • nuclease activity
  • endonuclease activity

  • Primary referencePhosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif., Klenchin VA, Czyz A, Goryshin IY, Gradman R, Lovell S, Rayment I, Reznikoff WS, Nucleic Acids Res. 2008 Oct;36(18):5855-62. Epub 2008 Sep 12. PMID:18790806
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (3ecp.pdb1.gz) 181 Kb
  • LPC: Ligand-Protein Contacts for 3ECP
  • CSU: Contacts of Structural Units for 3ECP
  • Likely Quarternary Molecular Structure file(s) for 3ECP
  • Structure Factors (219 Kb)
  • Retrieve 3ECP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ECP from S2C, [Save to disk]
  • Re-refined 3ecp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ECP 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 3ECP
  • 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 3ECP, from MSDmotif at EBI
  • Fold representative 3ecp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ecp_A] [3ecp_B] [3ecp_C] [3ecp]
  • SWISS-PROT database: [Q46731]
  • Domain organization of [TN5P_ECOLX] by SWISSPFAM
  • Other resources with information on 3ECP
  • Community annotation for 3ECP 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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