1OEJ

YodA from Escherichia coli crystallised with no added ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Yoda from Escherichia Coli is a Metal-Binding, Lipocalin-Like Protein

David, G.Blondeau, K.Schiltz, M.Penel, S.Lewit-Bentley, A.

(2003) J.Biol.Chem. 278: 43728

  • DOI: 10.1074/jbc.M304484200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have determined the crystal structure of YodA, an Escherichia coli protein of unknown function. YodA had been identified under conditions of cadmium stress, and we confirm that it binds metals such as cadmium and zinc. We have also found nickel bo ...

    We have determined the crystal structure of YodA, an Escherichia coli protein of unknown function. YodA had been identified under conditions of cadmium stress, and we confirm that it binds metals such as cadmium and zinc. We have also found nickel bound in one of the crystal forms. YodA is composed of two domains: a main lipocalin/calycin-like domain and a helical domain. The principal metal-binding site lies on one side of the calycin domain, thus making YodA the first metal-binding lipocalin known. Our experiments suggest that YodA expression may be part of a more general stress response. From sequence analogy with the C-terminal domain of a metal-binding receptor of a member of bacterial ATP-binding cassette transporters, we propose a three-dimensional model for this receptor and suggest that YodA may have a receptor-type partner in E. coli.


    Organizational Affiliation

    Laboratoire pour l'Utilisation du Rayonnement Electromagnétique, CNRS, CEA, MdR, BP. 34, 91898 Orsay Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN YODA
A
193Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: zinT (yodA)
Find proteins for P76344 (Escherichia coli (strain K12))
Go to UniProtKB:  P76344
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.348α = 90.00
b = 64.558β = 117.83
c = 41.499γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
CCP4phasing
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance