Macromolecule Content

Total Structure Weight: 125.80 kDa
Atom Count: 8915
Modelled Residue Count: 1132
Deposited Residue Count: 1144
Unique protein chains: 1

7DZ6

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

PDB DOI: 10.2210/pdb7DZ6/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: 2.10 Å
R-Value Free: 0.222
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis and molecular modification of D-allulose 3-epimerase from Sinorhizobium fredii

Zhu, Z.L., Takuya, M., Masaru, T., Lu, F.P., Qin, H.-M.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tagatose 3-epimerase	A, B, C, D	286	Sinorhizobium fredii CCBAU 83666	Mutation(s): 0 Gene Names: SF83666_b55120 EC: 5.1.3
UniProt
Find proteins for A0A249Q1V1 (Sinorhizobium fredii CCBAU 83666) Explore A0A249Q1V1 Go to UniProtKB: A0A249Q1V1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A249Q1V1
Protein Feature View Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.222
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.558	α = 90
b = 87.141	β = 99.387
c = 128.881	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2021-01-23
Released Date: 2022-08-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-08-03
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.