1LN4

CRYSTAL STRUCTURE OF E. COLI YHBY

• PDB DOI: https://doi.org/10.2210/pdb1LN4/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-05-02 Released: 2002-05-15 
• Deposition Author(s): Ostheimer, G.J., Barkan, A., Matthews, B.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins

Ostheimer, G.J., Barkan, A., Matthews, B.W.

(2002) Structure 10: 1593-1601

• PubMed: 12429100 
• DOI: https://doi.org/10.1016/s0969-2126(02)00886-9
• Primary Citation of Related Structures:  
  1LN4


• PubMed Abstract: 
  

  E. coli YhbY belongs to a conserved family of hypothetical proteins represented in eubacteria, archaea, and plants (Pfam code UPF0044). Three maize proteins harboring UPF0044-like domains are required for chloroplast group II intron splicing, and bioinformatic data suggest a role for prokaryotic UPF0044 members in translation. The crystal structure of YhbY has been determined. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Modeling studies indicate that the same surface is highly basic in all members of UPF0044, suggesting a conserved RNA binding surface. Taken together, the evidence suggests that members of UPF0044 constitute a previously unrecognized class of RNA binding domain.

---

Organizational Affiliation: 

Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.72 kDa 
• Atom Count: 876 
• Modelled Residue Count: 98 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yhbY	A	104	Escherichia coli	Mutation(s): 2  Gene Names: YHBY
UniProt
Find proteins for P0AGK4 (Escherichia coli (strain K12)) Explore P0AGK4  Go to UniProtKB:  P0AGK4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.324	α = 90
b = 57.324	β = 90
c = 70.895	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SOLVE	phasing
SCALA	data scaling
TNT	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-15 
Deposition Author(s): Ostheimer, G.J., Barkan, A., Matthews, B.W.

Revision History  

• Version 1.0: 2002-05-15
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection