3UIY

Crystal structure of SefD_dscA in H2O

• PDB DOI: https://doi.org/10.2210/pdb3UIY/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Enteritidis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-07 Released: 2012-05-02 
• Deposition Author(s): Garnett, J.A., Wei-chao, L., Liu, B., Matthews, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.332 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 

Literature

Promoting crystallisation of the Salmonella enteritidis fimbriae 14 pilin SefD using deuterium oxide.

Liu, B., Garnett, J.A., Lee, W.C., Lin, J., Salgado, P., Taylor, J., Xu, Y., Lambert, S., Cota, E., Matthews, S.

(2012) Biochem Biophys Res Commun 421: 208-213

• PubMed: 22497887 
• DOI: https://doi.org/10.1016/j.bbrc.2012.03.136
• Primary Citation of Related Structures:  
  3UIY, 3UIZ


• PubMed Abstract: 
  

  The use of heavy water (D(2)O) as a solvent is commonplace in many spectroscopic techniques for the study of biological macromolecules. A significant deuterium isotope effect exists where hydrogen-bonding is important, such as in protein stability, dynamics and assembly. Here we illustrate the use of D(2)O in additive screening for the production of reproducible diffraction-quality crystals for the Salmonella enteritidis fimbriae 14 (SEF14) putative tip adhesin, SefD.

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Organizational Affiliation: 

Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London SW7 2AZ, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.91 kDa 
• Atom Count: 935 
• Modelled Residue Count: 131 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of SefD and SefA	A	152	Salmonella enterica subsp. enterica serovar Enteritidis	Mutation(s): 0  Gene Names: sefD
UniProt
Find proteins for Q53997 (Salmonella enteritidis) Explore Q53997  Go to UniProtKB:  Q53997
Find proteins for P12061 (Salmonella enteritidis) Explore P12061  Go to UniProtKB:  P12061
UniProt Groups	Q53997P12061

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.332 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.48	α = 90
b = 52.48	β = 90
c = 218.03	γ = 120

Software Package:

Software Name	Purpose
Adxv	data processing
PHASER	phasing
REFMAC	refinement
xia2	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Garnett, J.A., Wei-chao, L., Liu, B., Matthews, S.J.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2013-01-09
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description