2ATS | pdb_00002ats

Dihydrodipicolinate synthase co-crystallised with (S)-lysine

• PDB DOI: https://doi.org/10.2210/pdb2ATS/pdb

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


• Deposited: 2005-08-26 Released: 2006-09-19 
• Deposition Author(s): Devenish, S.R.A., Dobson, R.C.J., Jameson, G.B., Gerrard, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

The co-crystallisation of (S)-lysine-bound dihydrodipicolinate synthase from E. coli indicates that domain movements are not responsible for (S)-lysine inhibition

Devenish, S.R.A., Dobson, R.C.J., Jameson, G.B., Gerrard, J.A.

To be published.

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: 63.2 kDa 
• Atom Count: 4,985 
• Modeled Residue Count: 584 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydrodipicolinate synthase	A, B	292	Escherichia coli	Mutation(s): 0  EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2  Go to UniProtKB:  P0A6L2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DLY	E [auth A], F [auth A], G [auth A]	D-LYSINE C6 H14 N2 O2 KDXKERNSBIXSRK-RXMQYKEDSA-N
K	C [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.68	α = 90
b = 121.68	β = 90
c = 109.799	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Devenish, S.R.A., Dobson, R.C.J., Jameson, G.B., Gerrard, J.A.

Revision History  

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations