7LOY | pdb_00007loy

Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum

• PDB DOI: https://doi.org/10.2210/pdb7LOY/pdb

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


• Deposited: 2021-02-11 Released: 2021-03-03 
• Deposition Author(s): Gilkes, J.M., Frampton, R.A., Board, A., Sheen, C.R., Smith, G.R., Dobson, R.C.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearum

Gilkes, J.M., Frampton, R.A., Board, A., 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, gel filtration

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: 191.27 kDa 
• Atom Count: 13,864 
• Modeled Residue Count: 1,770 
• Deposited Residue Count: 1,770 
• 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	295	Candidatus Liberibacter solanacearum	Mutation(s): 0  Gene Names: dapA EC: 4.3.3.7
UniProt
Find proteins for A0A0F4VK59 (Candidatus Liberibacter solanacearum) Explore A0A0F4VK59  Go to UniProtKB:  A0A0F4VK59

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.777	α = 90
b = 133.581	β = 100.55
c = 155.988	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 2.0: 2023-03-15
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.2: 2023-11-29
  Changes: Data collection