2ODM | pdb_00002odm

Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.283 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape.

Xu, L.Sedelnikova, S.E.Baker, P.J.Hunt, A.Errington, J.Rice, D.W.

(2007) Proteins 68: 438-455

  • DOI: https://doi.org/10.1002/prot.21377
  • Primary Citation Related Structures: 
    2ODM

  • PubMed Abstract: 

    The crystal structure of a conserved leucine rich protein, YlaN, from Staphylococcus aureus has been determined by X-ray crystallography to 2.3 A resolution. Whilst the precise function of S. aureus YlaN is unknown its homologue in B. subtilis has been shown to be essential for cell survival and is thought to be involved in controlling cell shape. The structure of S. aureus YlaN provides the first view of its protein family, which reveals that it is a novel homodimer whose subunit architecture is comprised of an antiparallel 3 helix bundle reminiscent of the helical arrangements seen in leucine zipper proteins. Analysis of the pattern of sequence conservation on the structure has led to the identification of two connected solvent exposed patches of conserved residues in each subunit located at one end of but on opposite faces of the molecule. We suggest that YlaN has a binding role in the cell rather than a catalytic function and a search for its ligand is underway to accelerate its exploitation as a target for antibiotic discovery.


  • Organizational Affiliation
    • Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 21.11 kDa 
  • Atom Count: 1,297 
  • Modeled Residue Count: 162 
  • Deposited Residue Count: 182 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UPF0358 protein MW0995
A, B
91Staphylococcus aureus subsp. aureus MW2Mutation(s): 4 
Gene Names: ylaN
UniProt
Find proteins for Q7A161 (Staphylococcus aureus (strain MW2))
Explore Q7A161 
Go to UniProtKB:  Q7A161
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7A161
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.425α = 90
b = 42.771β = 92.42
c = 62.593γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SOLVEphasing
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-10-30
    Changes: Structure summary