3DM9 Transport Protein date Jun 30, 2008
title Structures And Conformations In Solution Of The Signal Recog Particle Receptor From The Archaeon Pyrococcus Furiosus
authors P.F.Egea, H.Tsuruta, J.Napetschnig, P.Walter, R.M.Stroud
compound source
Molecule: Signal Recognition Particle Receptor
Chain: B
Synonym: Dpa
Engineered: Yes
 Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Strain: Dsm3638
Gene: Pf1766
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3) Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28b
symmetry Space Group: P 6 2 2
R_factor 0.203 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.600 144.600 70.413 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand MPD, MSE, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane., Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM, PLoS ONE. 2008;3(11):e3619. Epub 2008 Nov 3. PMID:18978942
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (3dm9.pdb1.gz) 302 Kb
  • Biological Unit Coordinates (3dm9.pdb2.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 3DM9
  • CSU: Contacts of Structural Units for 3DM9
  • Likely Quarternary Molecular Structure file(s) for 3DM9
  • Structure Factors (399 Kb)
  • Retrieve 3DM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DM9 from S2C, [Save to disk]
  • Re-refined 3dm9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DM9 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 3DM9
  • 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 3DM9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dm9_B] [3dm9]
  • SWISS-PROT database: [Q8U051]
  • Belongs to the general secretory pathway (sec) family according to TCDB.
  • Domain organization of [Q8U051_PYRFU] by SWISSPFAM
  • Domains found in 3DM9: [AAA] [SRP54] [SRP54_N ] by SMART
    • Other resources with information on 3DM9
  • Community annotation for 3DM9 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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