4BAC Transferase Dna date Sep 12, 2012
title Prototype Foamy Virus Strand Transfer Complexes On Product D
authors Z.Yin, M.Lapkouski, W.Yang, R.Craigie
compound source
Molecule: Integrase
Chain: A, B
Synonym: In, P42in
Ec: 2.7.7.49, 2.7.7.7, 3.1.26.13
Engineered: Yes
Organism_scientific: Human Spumaretrovirus
Organism_taxid: 11963
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b

Molecule: 5'-D(Aptptpgptpcpaptpgpgpapaptptp Tptpgptpap)-3';
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (38-Mer)
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Apgpgpapgpcpcpapapgpapcpgpgp 3';
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.185 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
160.617 160.617 125.092 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.26 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAssembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration., Yin Z, Lapkouski M, Yang W, Craigie R, Protein Sci. 2012 Sep 25. doi: 10.1002/pro.2166. PMID:23011895
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (120 Kb) [Save to disk]
  • Biological Unit Coordinates (4bac.pdb1.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 4BAC
  • CSU: Contacts of Structural Units for 4BAC
  • Structure Factors (342 Kb)
  • Retrieve 4BAC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BAC from S2C, [Save to disk]
  • Re-refined 4bac structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BAC 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 4BAC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4BAC, from MSDmotif at EBI
  • Fold representative 4bac from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bac_B] [4bac_A] [4bac_E] [4bac_D] [4bac_C] [4bac]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4BAC
  • Community annotation for 4BAC at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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