1OEK | pdb_00001oek

YodA from Escherichia coli crystallised with zinc ions

• PDB DOI: https://doi.org/10.2210/pdb1OEK/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2003-03-28 Released: 2003-08-15 
• Deposition Author(s): David, G., Blondeau, K., Renouard, M., Penel, S., Lewit-Bentley, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.351 (Depositor), 0.356 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.273 (Depositor) 

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 Biological Chem 278: 43728

• PubMed: 12909634 
• DOI: https://doi.org/10.1074/jbc.M304484200
• Primary Citation Related Structures: 
  1OEE, 1OEJ, 1OEK


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 22.64 kDa 
• Atom Count: 1,546 
• Modeled Residue Count: 185 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METAL-BINDING PROTEIN ZINT	A	193	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P76344 (Escherichia coli (strain K12)) Explore P76344  Go to UniProtKB:  P76344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.351 (Depositor), 0.356 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.273 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.6	α = 90
b = 58.6	β = 90
c = 152	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-15 
Deposition Author(s): David, G., Blondeau, K., Renouard, M., Penel, S., Lewit-Bentley, A.

Revision History  

• Version 1.0: 2003-08-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Data collection
• Version 1.4: 2024-11-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary