4UW0

Low resolution structure of WbdD with C-terminal bundle ordered to residue 505


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.87 Å
  • R-Value Free: 
    0.341 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.271 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAMClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

A Coiled-Coil Domain Acts as a Molecular Ruler to Regulate O-Antigen Chain Length in Lipopolysaccharide.

Hagelueken, G.Clarke, B.R.Huang, H.Tuukkanen, A.Danciu, I.Svergun, D.I.Hussain, R.Liu, H.Whitfield, C.Naismith, J.H.

(2015) Nat Struct Mol Biol 22: 50

  • DOI: https://doi.org/10.1038/nsmb.2935
  • Primary Citation of Related Structures:  
    4UW0

  • PubMed Abstract: 

    Long-chain bacterial polysaccharides have important roles in pathogenicity. In Escherichia coli O9a, a model for ABC transporter-dependent polysaccharide assembly, a large extracellular carbohydrate with a narrow size distribution is polymerized from monosaccharides by a complex of two proteins, WbdA (polymerase) and WbdD (terminating protein). Combining crystallography and small-angle X-ray scattering, we found that the C-terminal domain of WbdD contains an extended coiled-coil that physically separates WbdA from the catalytic domain of WbdD. The effects of insertions and deletions in the coiled-coil region were analyzed in vivo, revealing that polymer size is controlled by varying the length of the coiled-coil domain. Thus, the coiled-coil domain of WbdD functions as a molecular ruler that, along with WbdA:WbdD stoichiometry, controls the chain length of a model bacterial polysaccharide.


  • Organizational Affiliation

    Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WBDD505Escherichia coliMutation(s): 0 
Gene Names: EC3426_03072
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.87 Å
  • R-Value Free:  0.341 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.271 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.29α = 90
b = 181.29β = 90
c = 181.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2014-12-31
    Changes: Database references
  • Version 1.3: 2015-01-21
    Changes: Database references
  • Version 1.4: 2018-04-25
    Changes: Advisory, Data collection
  • Version 1.5: 2019-09-18
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.6: 2024-05-08
    Changes: Advisory, Data collection, Database references, Derived calculations, Other