4I1O Protein Transport Hydrolase date Nov 21, 2012
title Crystal Structure Of The Legionella Pneumophila Gap Domain O Complex With Rab1b Bound To Gdp And Bef3
authors E.M.Gazdag, A.Streller, I.R.Vetter, R.S.Goody, A.Itzen
compound source
Molecule: Ras-Related Protein Rab-1b
Chain: A, C, E, G
Fragment: Unp Residues 3-174
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab1b
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal

Molecule: Lepb
Chain: B, D, F, H
Fragment: Gap Domain (Unp Residues 317-618)
Engineered: Yes
Mutation: Yes

Organism_scientific: Legionella Pneumophila Subsp. Pneumoph
Organism_taxid: 272624
Strain: Philadelphia 1 Atcc 33152 Dsm 7513
Gene: Lepb, Lpg2490
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popinm
symmetry Space Group: P 31
R_factor 0.217 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.410 124.410 147.470 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand BEF, GDP, MG, PEG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, G, E


Primary referenceMechanism of Rab1b deactivation by the Legionella pneumophila GAP LepB., Mihai Gazdag E, Streller A, Haneburger I, Hilbi H, Vetter IR, Goody RS, Itzen A, EMBO Rep. 2013 Jan 4. doi: 10.1038/embor.2012.211. PMID:23288104
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (599 Kb) [Save to disk]
  • Biological Unit Coordinates (4i1o.pdb1.gz) 150 Kb
  • Biological Unit Coordinates (4i1o.pdb2.gz) 152 Kb
  • Biological Unit Coordinates (4i1o.pdb3.gz) 150 Kb
  • Biological Unit Coordinates (4i1o.pdb4.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 4I1O
  • CSU: Contacts of Structural Units for 4I1O
  • Structure Factors (535 Kb)
  • Retrieve 4I1O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I1O from S2C, [Save to disk]
  • Re-refined 4i1o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4I1O 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 4I1O
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4I1O, from MSDmotif at EBI
  • Fold representative 4i1o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i1o_E] [4i1o] [4i1o_C] [4i1o_D] [4i1o_G] [4i1o_H] [4i1o_A] [4i1o_B] [4i1o_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4I1O: [RAB ] by SMART
  • Other resources with information on 4I1O
  • Community annotation for 4I1O at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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