7DT1 | pdb_00007dt1

The structure of Lactobacillus fermentum 4,6-alpha-Glucanotransferase

• PDB DOI: https://doi.org/10.2210/pdb7DT1/pdb

• Classification: TRANSFERASE
• Organism(s): Limosilactobacillus fermentum
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2021-01-04 Released: 2022-01-12 
• Deposition Author(s): Yang, W.K., Yong, Y.H., Wu, L., Chen, S., Zhou, J.H., Wu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Characterization of a new 4,6-alpha-glucanotransferase from Limosilactobacillus fermentum NCC 3057 with ability of synthesizing low molecular mass isomalto-/maltopolysaccharide

Yang, W., Sheng, L., Chen, S., Wang, L., Su, L., Wu, J.

(2022) Food Biosci 46: 101514

• DOI: https://doi.org/10.1016/j.fbio.2021.101514

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 239.04 kDa 
• Atom Count: 14,678 
• Modeled Residue Count: 1,691 
• Deposited Residue Count: 2,094 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dextransucrase	A, B	1,047	Limosilactobacillus fermentum	Mutation(s): 0  EC: 2.4.1.5
UniProt
Find proteins for A0A1Z2RUD1 (Limosilactobacillus fermentum) Explore A0A1Z2RUD1  Go to UniProtKB:  A0A1Z2RUD1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	HA [auth A], IA [auth A], JB [auth B], KB [auth B], LB [auth B], MB [auth B], ZA [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	AB [auth B], CA [auth A], DA [auth A], FB [auth B], GB [auth B], Z [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	AA [auth A], BA [auth A], BB [auth B], CB [auth B], DB [auth B], EA [auth A], EB [auth B], FA [auth A], GA [auth A], H [auth A], HB [auth B], I [auth A], IB [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.83	α = 90
b = 106.08	β = 104.832
c = 106.02	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Yang, W.K., Yong, Y.H., Wu, L., Chen, S., Zhou, J.H., Wu, J.

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2022-08-10
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description