2O6D Membrane Protein, Protein Binding date Dec 07, 2006
title Structure Of Native Rtp34 From Treponema Pallidum
authors M.Machius, C.A.Brautigam, R.K.Deka, D.R.Tomchick, S.B.Lumpkins, M.V.Norgard
compound source
Molecule: 34 Kda Membrane Antigen
Chain: A, B
Synonym: Pathogen-Specific Membrane Antigen
Engineered: Yes
Mutation: Yes
 Organism_scientific: Treponema Pallidum
Organism_taxid: 160
Gene: Tpd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1-Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproexhta
symmetry Space Group: P 21 21 21
R_factor 0.188 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.071 65.881 150.605 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.86 Å
ligand CL, EDO, SO4, ZN enzyme
Primary referenceCrystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin., Deka RK, Brautigam CA, Tomson FL, Lumpkins SB, Tomchick DR, Machius M, Norgard MV, J Biol Chem. 2007 Feb 23;282(8):5944-58. Epub 2006 Dec 27. PMID:17192261
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (2o6d.pdb1.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 2O6D
  • CSU: Contacts of Structural Units for 2O6D
  • Likely Quarternary Molecular Structure file(s) for 2O6D
  • Structure Factors (417 Kb)
  • Retrieve 2O6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O6D from S2C, [Save to disk]
  • Re-refined 2o6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2O6D 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 2O6D
  • 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
  • 3D motif for 2O6D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o6d_B] [2o6d] [2o6d_A]
  • SWISS-PROT database: [P19478]
  • Domain organization of [TA34_TREPA] by SWISSPFAM
    • Other resources with information on 2O6D
  • Community annotation for 2O6D 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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