2IRV Membrane Protein date Oct 16, 2006
title Crystal Structure Of Glpg, A Rhomboid Intramembrane Serine P
authors E.Bibi, D.Fass, A.Ben-Shem
compound source
Molecule: Protein Glpg
Chain: A, B
Fragment: Protease Core, Residues 92-273
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Glpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C43(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.820 69.350 67.580 90.00 101.03 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand LDA, LMT, PGV, PO4 enzyme
note 2IRV (Molecule of the Month:pdb140)
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for intramembrane proteolysis by rhomboid serine proteases., Ben-Shem A, Fass D, Bibi E, Proc Natl Acad Sci U S A. 2006 Dec 26;. PMID:17190827
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (2irv.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (2irv.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 2IRV
  • CSU: Contacts of Structural Units for 2IRV
  • Likely Quarternary Molecular Structure file(s) for 2IRV
  • Structure Factors (319 Kb)
  • Retrieve 2IRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IRV from S2C, [Save to disk]
  • Re-refined 2irv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2IRV 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 2IRV
  • 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 2IRV, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2irv] [2irv_A] [2irv_B]
  • SWISS-PROT database: [P09391]
  • Belongs to the rhomboid protease (rhomboid) family according to TCDB.
  • Domain organization of [GLPG_ECOLI] by SWISSPFAM
    • Other resources with information on 2IRV
  • Community annotation for 2IRV 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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