2AXW | pdb_00002axw

Structure of DraD invasin from uropathogenic Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb2AXW/pdb

• Classification: CELL INVASION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-06 Released: 2005-11-01 
• Deposition Author(s): Jedrzejczak, R., Dauter, Z., Dauter, M., Piatek, R., Zalewska, B., Mroz, M., Bury, K., Nowicki, B., Kur, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.168 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Structure of DraD invasin from uropathogenic Escherichia coli: a dimer with swapped beta-tails.

Jedrzejczak, R., Dauter, Z., Dauter, M., Piatek, R., Zalewska, B., Mroz, M., Bury, K., Nowicki, B., Kur, J.

(2006) Acta Crystallogr D Biol Crystallogr 62: 157-164

• PubMed: 16421447 
• DOI: https://doi.org/10.1107/S0907444905036747
• Primary Citation Related Structures: 
  2AXW


• PubMed Abstract: 
  

  The dra gene cluster of uropathogenic strains of Escherichia coli produces proteins involved in bacterial attachment to and invasion of the eukaryotic host tissues. The crystal structure of a construct of E. coli DraD possessing an additional C-terminal extension of 13 amino acids, including a His6 tag, has been solved at a resolution of 1.05 angstroms. The protein forms symmetric dimers through the exchange of the C-terminal beta-strands, which participate in the immunoglobulin-like beta-sandwich fold of each subunit. This structure confirms that DraD is able to act as an acceptor in the donor-strand complementation mechanism of fiber formation but, in contrast to DraE adhesin, its native sequence does not have a donor strand; therefore, DraD can only be located at the tip of the fiber.

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Organizational Affiliation: 
• Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.55 kDa 
• Atom Count: 2,412 
• Modeled Residue Count: 268 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DraD invasin	A, B	134	Escherichia coli	Mutation(s): 0  Gene Names: draD
UniProt
Find proteins for Q47038 (Escherichia coli) Explore Q47038  Go to UniProtKB:  Q47038

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.168 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.59	α = 90
b = 61.82	β = 90
c = 112.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-01 
Deposition Author(s): Jedrzejczak, R., Dauter, Z., Dauter, M., Piatek, R., Zalewska, B., Mroz, M., Bury, K., Nowicki, B., Kur, J.

Revision History  

• Version 1.0: 2005-11-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary