7LVL | pdb_00007lvl

Dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine from Candidatus Liberibacter solanacearum

• PDB DOI: https://doi.org/10.2210/pdb7LVL/pdb

• Classification: LYASE
• Organism(s): Candidatus Liberibacter solanacearum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-02-25 Released: 2021-03-10 
• Deposition Author(s): Gilkes, J.M., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine from Candidatus Liberibacter solanacearum

Gilkes, J.M., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.D.

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)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 197.06 kDa 
• Atom Count: 14,340 
• Modeled Residue Count: 1,776 
• Deposited Residue Count: 1,812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E, F	302	Candidatus Liberibacter solanacearum	Mutation(s): 0  Gene Names: dapA, DJ66_0589 EC: 4.3.3.7
UniProt
Find proteins for A0A0F4VK59 (Candidatus Liberibacter solanacearum) Explore A0A0F4VK59  Go to UniProtKB:  A0A0F4VK59

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.763	α = 90
b = 133.484	β = 100.45
c = 155.778	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Gilkes, J.M., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.D.

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description