9OUB | pdb_00009oub

Structure of full-length Streptococcus mutans GtfD in complex with dextran 1000 in domain V

• PDB DOI: https://doi.org/10.2210/pdb9OUB/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-28 Released: 2026-04-22 
• Deposition Author(s): Schormann, N., Deivanayagam, C.
• Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.284 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Analysis of Streptococcus mutans GtfD-FL (GTF-S)

Schormann, N., Deivanayagam, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 162.8 kDa 
• Atom Count: 10,238 
• Modeled Residue Count: 1,284 
• Deposited Residue Count: 1,438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyltransferase-S	A	1,438	Streptococcus mutans	Mutation(s): 0  Gene Names: gtfD, SMU_910 EC: 2.4.1.5
UniProt
Find proteins for P49331 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore P49331  Go to UniProtKB:  P49331

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan: G62200YG GlyCosmos: G62200YG GlyGen: G62200YG

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G69864PN GlyCosmos: G69864PN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.284 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.841	α = 90
b = 95.485	β = 90
c = 175.326	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Schormann, N., Deivanayagam, C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	1R01DE033232-01A1

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release