6FI8 Dna Binding Protein date Jan 17, 2018
title Crystal Structure Of The Is608 Transposase In Complex With L 29-Mer Dna Hairpin And A 6-Mer Dna Representing The Intact Site: Pre-Cleavage Target Capture Complex
authors N.R.Morero, O.Barabas
compound source
Molecule: Putative Transposase
Chain: A, B, G, H
Synonym: Transposase,Transposase Orfa
Engineered: Yes
Organism_scientific: Helicobacter Pylori
Organism_common: Campylobacter Pylori
Organism_taxid: 210
Gene: Bb387_02765, Bb390_06935, Bb392_05440, Bb394_07800, Bb413_07925, Bb437_07715, Bb438_04880, Bb447_07970, Bb453_0 Bb461_01775, Bb469_00740, Bfr58_04045, Bfr58_04080, Bfr58_0 Bfr58_07690, Bfr58_08055, Bgl67_05025, Bgl76_01750, Bgl76_0 Bgl76_01830, Bgl76_03945, Bgl76_04370, Bgl76_05875, Bgl76_0 Bgl85_00790;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna 29-Mer (Le29)
Chain: C, D, I, J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Helicobacter Pylori
Organism_taxid: 210

Molecule: Dna 6-Mer (T6')
Chain: E, F, K, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Helicobacter Pylori
Organism_taxid: 210
symmetry Space Group: P 41 21 2
R_factor 0.197 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.640 138.640 117.950 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA enzyme
Gene
Ontology
ChainFunctionProcessComponent
H, A, G, B


Primary referenceTargeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering., Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S, Guynet C, Hickman AB, Chandler M, Dyda F, Barabas O, Nucleic Acids Res. 2018 Apr 9. pii: 4964819. doi: 10.1093/nar/gky235. PMID:29635476
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (299 Kb) [Save to disk]
  • Biological Unit Coordinates (6fi8.pdb1.gz) 145 Kb
  • Biological Unit Coordinates (6fi8.pdb2.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 6FI8
  • CSU: Contacts of Structural Units for 6FI8
  • Structure Factors (833 Kb)
  • Retrieve 6FI8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FI8 from S2C, [Save to disk]
  • View 6FI8 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 6FI8
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6fi8_B] [6fi8_C] [6fi8_J] [6fi8_F] [6fi8_I] [6fi8_D] [6fi8_G] [6fi8_K] [6fi8_L] [6fi8_A] [6fi8_E] [6fi8_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FI8
  • Community annotation for 6FI8 at PDBWiki (http://pdbwiki.org)

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