7DZ5

Crystal structures of D-allulose 3-epimerase with D-sorbose from Sinorhizobium fredii

PDB DOI: https://doi.org/10.2210/pdb7DZ5/pdb

Classification: ISOMERASE
Organism(s): Sinorhizobium fredii CCBAU 83666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-23 Released: 2022-08-03
Deposition Author(s): Zhu, Z.L., Miyakawa, T., Tanokura, M., Lu, F.P., Qin, H.-M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.178
R-Value Work: 0.153
R-Value Observed: 0.154

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

Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening

Li, C., Gao, X., Qi, H., Zhang, W., Li, L., Wei, C., Wei, M., Sun, X., Wang, S., Wang, L., Ji, Y., Mao, S., Zhu, Z., Tanokura, M., Lu, F., Qin, H.M.

(2023) Angew Chem Int Ed Engl

DOI: https://doi.org/10.1002/anie.202216721

Macromolecule Content

Total Structure Weight: 125.5 kDa
Atom Count: 9,444
Modelled Residue Count: 1,130
Deposited Residue Count: 1,132
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	283	Sinorhizobium fredii CCBAU 83666	Mutation(s): 0 Gene Names: SF83666_b55120
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

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