2Q9T | pdb_00002q9t

High-resolution structure of the DING protein from Pseudomonas fluorescens

• PDB DOI: https://doi.org/10.2210/pdb2Q9T/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pseudomonas fluorescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-14 Released: 2008-06-17 
• Deposition Author(s): Moniot, S., Ahn, S., Elias, M., Kim, D., Scott, K., Chabriere, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Structure-function relationships in a bacterial DING protein.

Ahn, S., Moniot, S., Elias, M., Chabriere, E., Kim, D., Scott, K.

(2007) FEBS Lett 581: 3455-3460

• PubMed: 17612529 
• DOI: https://doi.org/10.1016/j.febslet.2007.06.050
• Primary Citation Related Structures: 
  2Q9T


• PubMed Abstract: 
  

  A recombinant DING protein from Pseudomonas fluorescens has been previously shown to have a phosphate-binding site, and to be mitogenic for human cells. Here we report the three-dimensional structure of the protein, confirming a close similarity to the "Venus flytrap" structure seen in other human and bacterial phosphate-binding proteins. Site-directed mutagenesis confirms the role of a key residue involved in phosphate binding, and that the mitogenic activity is not dependent on this property. Deletion of one of the two hinged domains that constitute the Venus flytrap also eliminates phosphate binding whilst enhancing mitogenic activity.

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Organizational Affiliation: 
• School of Biological Sciences, The University of Auckland, Auckland, New Zealand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.78 kDa 
• Atom Count: 3,742 
• Modeled Residue Count: 374 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DING	A	379	Pseudomonas fluorescens	Mutation(s): 0
UniProt
Find proteins for D0VWY2 (Pseudomonas fluorescens (strain SBW25)) Explore D0VWY2  Go to UniProtKB:  D0VWY2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.728	α = 90
b = 123.679	β = 116.71
c = 40.833	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Moniot, S., Ahn, S., Elias, M., Kim, D., Scott, K., Chabriere, E.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary