4FHA

Structure of Dihydrodipicolinate Synthase from Streptococcus pneumoniae,bound to pyruvate and lysine

• PDB DOI: https://doi.org/10.2210/pdb4FHA/pdb

• Classification: LYASE
• Organism(s): Streptococcus pneumoniae SP3-BS71
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-06 Released: 2013-09-18 
• Deposition Author(s): Perugini, M.A., Dogovski, C., Parker, M.W., Gorman, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.183 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae

Perugini, M.A., Dogovski, C., Parker, M.W., Gorman, M.A., Dobson, R.C.J., Jameson, G.B., Ketaren, N.E., Praszkier, J., Bailey, M.F., Bryant, G., Yang, J., Griffin, M.D.W., Pearce, F.G., Mitsakos, V.

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: 68.37 kDa 
• Atom Count: 5,087 
• Modelled Residue Count: 614 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	311	Streptococcus pneumoniae SP3-BS71	Mutation(s): 0  Gene Names: CGSSp3BS71_00085 EC: 4.2.1.52

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	C [auth A], E [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.183 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.381	α = 90
b = 106.368	β = 90
c = 106.232	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Perugini, M.A., Dogovski, C., Parker, M.W., Gorman, M.A.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-29
  Changes: Data collection