5F4W

Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with TBP

• PDB DOI: https://doi.org/10.2210/pdb5F4W/pdb

• Classification: LYASE
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-03 Released: 2017-02-01 
• Deposition Author(s): LowKam, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.206 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE

LowKam, C., Liotard, B., Sygusch, 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 147.29 kDa 
• Atom Count: 11,921 
• Modelled Residue Count: 1,302 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase 2	A, B, C, D	327	Streptococcus pyogenes serotype M1	Mutation(s): 0  Gene Names: lacD2, lacD.2, SPy_1919, M5005_Spy1635 EC: 4.1.2.40
UniProt
Find proteins for P63705 (Streptococcus pyogenes serotype M1) Explore P63705  Go to UniProtKB:  P63705

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6T	E [auth A]	1,6-di-O-phosphono-D-tagatose C6 H14 O12 P2 XPYBSIWDXQFNMH-PQLUHFTBSA-N
13P	G [auth A]	1,3-DIHYDROXYACETONEPHOSPHATE C3 H7 O6 P GNGACRATGGDKBX-UHFFFAOYSA-N
CA	H [auth A], I [auth A], K [auth C], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], J [auth B], L [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.206 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.955	α = 90
b = 107.373	β = 90
c = 237.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): LowKam, C.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description