8XIV | pdb_00008xiv

Production of D-psicose

• PDB DOI: https://doi.org/10.2210/pdb8XIV/pdb

• Classification: ISOMERASE
• Organism(s): Kroppenstedtia eburnea
• Expression System: Kroppenstedtia eburnea
• Mutation(s): No 


• Deposited: 2023-12-20 Released: 2024-12-25 
• Deposition Author(s): Guo, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.196 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Production of D-psicose

Guo, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.54 kDa 
• Atom Count: 2,716 
• Modeled Residue Count: 290 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tagatose 3-epimerase	A	290	Kroppenstedtia eburnea	Mutation(s): 0  Gene Names: SAMN05421790_10663
UniProt
Find proteins for A0A1N7MFN7 (Kroppenstedtia eburnea) Explore A0A1N7MFN7  Go to UniProtKB:  A0A1N7MFN7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUD (Subject of Investigation/LOI)	B [auth A]	D-fructose C6 H12 O6 BJHIKXHVCXFQLS-UYFOZJQFSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO (Subject of Investigation/LOI)	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.196 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.056	α = 90
b = 121.056	β = 90
c = 47.433	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Guo, D.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release