7MJF | pdb_00007mjf

Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

• PDB DOI: https://doi.org/10.2210/pdb7MJF/pdb

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


• Deposited: 2021-04-20 Released: 2021-07-14 
• Deposition Author(s): Gilkes, J., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.208 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

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

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)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 193.48 kDa 
• Atom Count: 14,512 
• Modeled Residue Count: 1,776 
• Deposited Residue Count: 1,776 
• 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	296	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZGM	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], Q [auth F]	(4S)-4-hydroxy-2-oxoheptanedioic acid C7 H10 O6 HNOAJOYERZTSNK-BYPYZUCNSA-N
E8U	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], R [auth F]	(4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid C7 H10 O6 HNOAJOYERZTSNK-SCSAIBSYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.208 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.101	α = 90
b = 132.881	β = 99.96
c = 155.062	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Gilkes, J., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-03-13
  Changes: Source and taxonomy
• Version 1.3: 2024-10-30
  Changes: Structure summary