4D1Q Protein-Dna Complex date May 04, 2014
title Hermes Transposase Bound To Its Terminal Inverted Repeat
authors A.B.Hickman, H.Ewis, X.Li, J.Knapp, T.Laver, A.L.Doss, G.Tolun, A.S A.Grishaev, A.Bax, P.Atkinson, N.L.Craig, F.Dyda
compound source
Molecule: Transposase
Chain: A, B, G, H
Fragment: Dimerization, Catalytic And Insertion Domains, Re 612;
Synonym: Hermes Transposase
Engineered: Yes
Mutation: Yes
Organism_scientific: Musca Domestica
Organism_common: House Fly
Organism_taxid: 7370
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Top10
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbadmyc-His

Molecule: Terminal Inverted Repeat
Chain: C, E, I, K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Musca Domestica
Organism_common: House Fly
Organism_taxid: 7370

Molecule: Terminal Inverted Repeat
Chain: D, F, J, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Musca Domestica
Organism_common: House Fly
Organism_taxid: 7370
symmetry Space Group: P 32 2 1
R_factor 0.212 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
265.150 265.150 157.640 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.40 Å
ligand NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
H, A, G, B


Primary referenceStructural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica., Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss AL, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F, Cell. 2014 Jul 17;158(2):353-67. doi: 10.1016/j.cell.2014.05.037. PMID:25036632
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (387 Kb) [Save to disk]
  • Biological Unit Coordinates (4d1q.pdb1.gz) 756 Kb
  • LPC: Ligand-Protein Contacts for 4D1Q
  • CSU: Contacts of Structural Units for 4D1Q
  • Structure Factors (839 Kb)
  • Retrieve 4D1Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D1Q from S2C, [Save to disk]
  • Re-refined 4d1q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D1Q 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 4D1Q
  • 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 4D1Q, from MSDmotif at EBI
  • Fold representative 4d1q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d1q_A] [4d1q_I] [4d1q_J] [4d1q_C] [4d1q_D] [4d1q_H] [4d1q_G] [4d1q_L] [4d1q] [4d1q_K] [4d1q_B] [4d1q_E] [4d1q_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4D1Q
  • Community annotation for 4D1Q at PDBWiki (http://pdbwiki.org)

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