4I7V | pdb_00004i7v

Agrobacterium tumefaciens DHDPS with pyruvate

• PDB DOI: https://doi.org/10.2210/pdb4I7V/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: 1.45 Å
• R-Value Free: 
  0.180 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

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: 131.9 kDa 
• Atom Count: 10,239 
• Modeled Residue Count: 1,175 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D	308	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: dapA, AGROH133_05014 EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q8UGL3 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8UGL3  Go to UniProtKB:  Q8UGL3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.180 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.77	α = 90
b = 77.03	β = 121.16
c = 98.94	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
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary