2VJV Dna-Binding Protein date Dec 13, 2007
title Crystal Structure Of The Is608 Transposase In Complex With Left End 26-Mer Dna Hairpin And A 6-Mer Dna Representing The Left End Cleavage Site
authors O.Barabas, D.R.Ronning, C.Guynet, A.B.Hickman, B.Ton-Hoang, M.Chandler, F.Dyda
compound source
Molecule: Transposase Orfa
Chain: A, B
Fragment: Residues 2-155
Synonym: Is608 Transposase
Engineered: Yes
Organism_scientific: Helicobacter Pylori
Organism_taxid: 210
Strain: Pecan2a
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Pet32b

Molecule: 5'-D(Dadadadgdcdcdcdcdtdadgdcdtpdt Dtdtdadgdcdtdadtdgdgdgdgp)-3';
Chain: C, D
Synonym: Left End 26-Mer Hairpin

Synthetic: Yes
Organism_scientific: Helicobacter Pylori
Organism_taxid: 210
Strain: Pecan2a

Molecule: 5'-D(Dtdadtdtdadcp)-3'
Chain: E, F
Synonym: 6-Mer Left End Cleavage Site

Synthetic: Yes
Organism_scientific: Helicobacter Pylori
Organism_taxid: 210
Strain: Pecan2a
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
66.292 72.407 110.174 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand MG enzyme
A, B

Primary referenceMechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection., Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F, Cell. 2008 Jan 25;132(2):208-20. PMID:18243097
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2vjv.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2VJV
  • CSU: Contacts of Structural Units for 2VJV
  • Likely Quarternary Molecular Structure file(s) for 2VJV
  • Structure Factors (263 Kb)
  • Retrieve 2VJV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VJV from S2C, [Save to disk]
  • Re-refined 2vjv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VJV 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 2VJV
  • 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 2VJV, from MSDmotif at EBI
  • Fold representative 2vjv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vjv_A] [2vjv_F] [2vjv_C] [2vjv_E] [2vjv] [2vjv_D] [2vjv_B]
  • SWISS-PROT database: [Q933Z0]
  • Domain organization of [Q933Z0_HELPY] by SWISSPFAM
  • Domain found in 2VJV: [Y1_Tnp ] by SMART
  • Other resources with information on 2VJV
  • Community annotation for 2VJV 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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