1YHD | pdb_00001yhd

The solution structure of YGGX from Escherichia Coli

• PDB DOI: https://doi.org/10.2210/pdb1YHD/pdb
• BMRB: 6453

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-01-07 Released: 2005-01-18 
• Deposition Author(s): Osborne, M.J., Siddiqui, N., Landgraf, D., Pomposiello, P.J., Gehring, K.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function 

Literature

The solution structure of the oxidative stress-related protein YggX from Escherichia coli.

Osborne, M.J., Siddiqui, N., Landgraf, D., Pomposiello, P.J., Gehring, K.

(2005) Protein Sci 14: 1673-1678

• PubMed: 15883188 
• DOI: https://doi.org/10.1110/ps.051358105
• Primary Citation Related Structures: 
  1YHD


• PubMed Abstract: 
  

  YggX is a highly conserved protein found only in eubacteria and is proposed to be involved in the bacterial response to oxidative stress. Here we report the solution structure of YggX from Escherichia coli determined by nuclear magnetic resonance spectroscopy. The structure of YggX displays a fold consisting of two N-terminal antiparallel beta-sheets and three alpha-helices, which shares significant structural similarity to the crystal structure of a hypothetical protein PA5148 from Pseudomonas aeruginosa. Previous studies propose YggX as an iron binding protein that is involved in cellular iron trafficking. Our data indicate that the protein alone does not bind iron in vitro, suggesting other cofactors or different conditions may be necessary for metal binding.

---

Organizational Affiliation: 
• Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.1 kDa 
• Atom Count: 772 
• Modeled Residue Count: 92 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0269 protein yggX	A	100	Escherichia coli	Mutation(s): 0  Gene Names: YGGX
UniProt
Find proteins for P0A8P3 (Escherichia coli (strain K12)) Explore P0A8P3  Go to UniProtKB:  P0A8P3

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Osborne, M.J., Siddiqui, N., Landgraf, D., Pomposiello, P.J., Gehring, K.

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection