5VFX Dna Binding Protein Dna date Apr 10, 2017
title Structure Of An Accessory Protein Of The Pcw3 Relaxosome In With The Origin Of Transfer (Orit) Dna
authors D.A.K.Traore, J.A.Wisniewski, S.F.Flanigan, P.J.Conroy, S.Panjik F.Mok, C.Lao, M.D.W.Griffin, V.Adams, J.I.Rood, J.C.Whisstock
compound source
Molecule: Tcpk
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502
Gene: Ers852446_03033, Pbeta2_00022, Pcpb2-Cp1_20, Pcw3_002 Ne10_20, Pnetb_00021, Ptet_021;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgl12

Molecule: Orit
Chain: I, K, N, O
Engineered: Yes

Synthetic: Yes
Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502

Molecule: Orit
Chain: J, L, M, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502
symmetry Space Group: P 1 21 1
R_factor 0.198 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.503 109.894 122.780 90.00 93.02 90.00
method X-Ray Diffractionresolution 2.81 Å
Primary referenceCrystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3., Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ, Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI, Whisstock JC, Nat Commun. 2018 Sep 13;9(1):3732. doi: 10.1038/s41467-018-06096-2. PMID:30213934
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (5vfx.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (5vfx.pdb2.gz) 102 Kb
  • CSU: Contacts of Structural Units for 5VFX
  • Structure Factors (1543 Kb)
  • Retrieve 5VFX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VFX from S2C, [Save to disk]
  • View 5VFX 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 5VFX
  • 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: [5vfx_E] [5vfx_B] [5vfx_L] [5vfx_F] [5vfx_I] [5vfx_J] [5vfx_C] [5vfx_O] [5vfx_H] [5vfx_P] [5vfx_K] [5vfx_G] [5vfx_D] [5vfx_N] [5vfx_A] [5vfx_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VFX
  • Community annotation for 5VFX at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science