8XJ1 | pdb_00008xj1

Structure of Apo-KeDt3e

• PDB DOI: https://doi.org/10.2210/pdb8XJ1/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.Y.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Production of D-psicose

Guo, D.Y.

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: 33.03 kDa 
• Atom Count: 2,391 
• Modeled Residue Count: 288 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tagatose 3-epimerase	A	289	Kroppenstedtia eburnea	Mutation(s): 0  Gene Names: SAMN05421790_10663
UniProt
Find proteins for A0A1N7MFN7 (Kroppenstedtia eburnea) Explore A0A1N7MFN7  Go to UniProtKB:  A0A1N7MFN7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.31	α = 90
b = 119.31	β = 90
c = 47.87	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.Y.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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