3RF3	Protein Binding Toxin	date	Apr 05, 2011
title	Shigella Ipaa-Vbs3 In Complex With Human Vinculin
authors	H.Park, A.Sharff, T.Izard
compound		source
Molecule: Vinculin Chain: A, B Fragment: Unp Residues 1-258 Synonym: Metavinculin Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vcl, Vinculin Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Invasin Ipaa Chain: C, D Fragment: Unp Residues 488-512 Synonym: 70 Kda Antigen Engineered: Yes		Organism_scientific: Shigella Flexneri Organism_taxid: 623 Gene: Cp0125, Ipaa Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
symmetry	Space Group: P 21 21 21	R_factor 0.184 R_Free 0.195
crystal cell	length a length b length c angle alpha angle beta angle gamma 53.583 85.319 137.904 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.61 Å
ligand	CAC	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	Novel vinculin binding site of the IpaA invasin of Shigella., Park H, Valencia-Gallardo C, Sharff A, Tran Van Nhieu G, Izard T, J Biol Chem. 2011 Jul 1;286(26):23214-21. Epub 2011 Apr 27. PMID:21525010

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (384 Kb) [Save to disk] Biological Unit Coordinates (3rf3.pdb1.gz) 189 Kb Biological Unit Coordinates (3rf3.pdb2.gz) 191 Kb Biological Unit Coordinates (3rf3.pdb3.gz) 379 Kb LPC: Ligand-Protein Contacts for 3RF3 CSU: Contacts of Structural Units for 3RF3 Structure Factors (1704 Kb) Retrieve 3RF3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3RF3 from S2C, [Save to disk] Re-refined 3rf3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3RF3 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 3RF3

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 3RF3, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3rf3_A] [3rf3_D] [3rf3_C] [3rf3_B] [3rf3] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3RF3

Community annotation for 3RF3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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