3IV3 | pdb_00003iv3

The Structure of a putative tagatose 1,6-aldolase from Streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb3IV3/pdb

• Classification: LYASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-09-22 
• Deposition Author(s): Cuff, M.E., Hatzos, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.176 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

The Structure of a putative tagatose 1,6-aldolase from Streptococcus mutans

Cuff, M.E., Hatzos, C., Jedrzejczak, R., Joachimiak, A.

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: 37.86 kDa 
• Atom Count: 3,045 
• Modeled Residue Count: 329 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase 2	A	332	Streptococcus mutans	Mutation(s): 0  Gene Names: lacD2, SMU_116 EC: 4.1.2.40
UniProt
Find proteins for Q8DWE5 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DWE5  Go to UniProtKB:  Q8DWE5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	C [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.176 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.214	α = 90
b = 113.759	β = 90
c = 74.399	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Cuff, M.E., Hatzos, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary