5F2M | pdb_00005f2m

Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with competitive inhibitor hexitol-1,6-bisphosphate

• PDB DOI: https://doi.org/10.2210/pdb5F2M/pdb

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


• Deposited: 2015-12-02 Released: 2016-12-07 
• Deposition Author(s): LowKam, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

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: 147.22 kDa 
• Atom Count: 11,864 
• Modeled Residue Count: 1,300 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M2P	E [auth A]	D-MANNITOL-1,6-DIPHOSPHATE C6 H16 O12 P2 WOYYTQHMNDWRCW-KVTDHHQDSA-N
CA	F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth D], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.985	α = 90
b = 107.837	β = 90
c = 237.81	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: 2016-12-07 
Deposition Author(s): LowKam, C.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description