4I7W

Agrobacterium tumefaciens DHDPS with lysine and pyruvate

• PDB DOI: https://doi.org/10.2210/pdb4I7W/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-01 Released: 2013-12-04 
• Deposition Author(s): Atkinson, S.C., Dogovski, C., Dobson, R.C.J., Perugini, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.186 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

Structure, function and allostery of the bona fide DHDPS from the plant pathogen Agrobacterium tumefaciens

Atkinson, S.C., Dogovski, C., Dobson, R.C.J., Perugini, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 66.34 kDa 
• Atom Count: 5,501 
• Modelled Residue Count: 588 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	308	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: dapA, AGROH133_05014 EC: 4.2.1.52

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	C [auth A], D [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A, B	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.186 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.09	α = 90
b = 122.78	β = 90
c = 129.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Atkinson, S.C., Dogovski, C., Dobson, R.C.J., Perugini, M.A.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release