3DMD 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, A, C
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: Pet28b
symmetry Space Group: C 1 2 1
R_factor 0.189 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
149.956 102.368 101.766 90.00 119.81 90.00
method X-Ray Diffractionresolution 2.21 Å
ligand GOL, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, 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] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (3dmd.pdb1.gz) 316 Kb
  • Biological Unit Coordinates (3dmd.pdb2.gz) 56 Kb
  • Biological Unit Coordinates (3dmd.pdb3.gz) 54 Kb
  • Biological Unit Coordinates (3dmd.pdb4.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 3DMD
  • CSU: Contacts of Structural Units for 3DMD
  • Likely Quarternary Molecular Structure file(s) for 3DMD
  • Structure Factors (521 Kb)
  • Retrieve 3DMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DMD from S2C, [Save to disk]
  • Re-refined 3dmd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DMD 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 3DMD
  • 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 3DMD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dmd_A] [3dmd_C] [3dmd_B] [3dmd]
  • 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 3DMD: [AAA] [SRP54] [SRP54_N ] by SMART
    • Other resources with information on 3DMD
  • Community annotation for 3DMD 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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