7X7W

The X-ray Crystallographic Structure of D-Psicose 3-epimerase from Clostridia bacterium

• PDB DOI: https://doi.org/10.2210/pdb7X7W/pdb

• Classification: ISOMERASE
• Organism(s): Clostridia bacterium
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2022-03-10 Released: 2022-09-07 
• Deposition Author(s): Li, Z.F., Ban, X.F., Xie, X.F., Tian, Y.X., Li, C.M., Gu, Z.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

Crystal structure of a novel homodimeric D-allulose 3-epimerase from a Clostridia bacterium

Xie, X., Tian, Y., Ban, X., Li, C., Yang, H., Li, Z.

(2022) Acta Crystallogr D Biol Crystallogr 78: 1180-1191

• DOI: https://doi.org/10.1107/S2059798322007707

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.81 kDa 
• Atom Count: 4,705 
• Modelled Residue Count: 576 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-PSICOSE 3-EPIMERASE	A, B	288	Clostridia bacterium	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.018	α = 90
b = 70.657	β = 99.32
c = 153.784	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Li, Z.F., Ban, X.F., Xie, X.F., Tian, Y.X., Li, C.M., Gu, Z.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31722040
National Natural Science Foundation of China (NSFC)	China	31771935
National Natural Science Foundation of China (NSFC)	China	31901628

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2022-09-14
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description