7DT1

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.256
R-Value Work: 0.194
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Z2RUD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain ZA [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain ZA [auth B]	HA [auth A] IA [auth A] JB [auth B] KB [auth B] LB [auth B] 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		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain ZA [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain Z [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain Z [auth A]	AB [auth B] CA [auth A] DA [auth A] FB [auth B] GB [auth B] 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		Interactions Focus chain AB [auth B] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth B] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain Z [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B]	AA [auth A] BA [auth A] BB [auth B] CB [auth B] DB [auth B] 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		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.256
R-Value Work: 0.194
R-Value Observed: 0.197
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Revision History (Full details and data files)

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