5HJL

Crystal structure of class I tagatose 1,6-bisphosphate aldolase LacD from Streptococcus porcinus

• PDB DOI: https://doi.org/10.2210/pdb5HJL/pdb

• Classification: LYASE
• Organism(s): Streptococcus porcinus str. Jelinkova 176
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-13 Released: 2016-12-07 
• Deposition Author(s): Freichels, R., Kerff, F., Herman, R., Charlier, P., Galleni, M.
• Funding Organization(s): National Fund for Scientific Research, FRS-FNRS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.229 
• R-Value Work: 0.174 

Starting Model: experimental

Literature

Structure and Characterization of a new class I Tagatose-1,6-bipshosphate aldolase from Streptococcus porcinus : switch in specificity directed by an Arginine

Freichels, R., Delmarcelle, M., Van der Heiden, E., Herman, R., Colarusso, A., Wathelet, B., Kerff, F., Galleni, M.

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: 74.5 kDa 
• Atom Count: 5,054 
• Modelled Residue Count: 644 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase	A, B	333	Streptococcus porcinus str. Jelinkova 176	Mutation(s): 0  Gene Names: lacD, STRPO_0644 EC: 4.1.2.40

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.229 
• R-Value Work: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.66	α = 90
b = 93.75	β = 120.58
c = 88.11	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Freichels, R., Kerff, F., Herman, R., Charlier, P., Galleni, M.

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Funding Organization	Location	Grant Number
National Fund for Scientific Research	Belgium	--
FRS-FNRS	Belgium	IISN 4.4503

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description