7ERN | pdb_00007ern

Crystal structure of D-allulose 3-epimerase with D-fructose from Agrobacterium sp. SUL3

PDB DOI: https://doi.org/10.2210/pdb7ERN/pdb

Classification: ISOMERASE
Organism(s): Agrobacterium sp. SUL3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-06 Released: 2022-05-11
Deposition Author(s): Zhu, Z.L., Miyakawa, T., Tanokura, M., Lu, F.P., Qin, H.-M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform

Li, C., Gao, H., Li, H., Wang, T., Lu, F.P., Qin, H.-M.

(2024) Adv Sci (Weinh)

DOI: https://doi.org/10.1002/advs.202306478

Macromolecule Content

Total Structure Weight: 123.16 kDa
Atom Count: 8,981
Modeled Residue Count: 1,133
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tagatose 3-epimerase	A, B, C, D	284	Agrobacterium sp. SUL3	Mutation(s): 0 Gene Names: AKG12_23230 EC: 5.1.3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUD (Subject of Investigation/LOI) Query on FUD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	D-fructose C₆ H₁₂ O₆ BJHIKXHVCXFQLS-UYFOZJQFSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]