8I83

Crystal Structure of phosphinothricin dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb8I83/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lysinibacillus composti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-03 Released: 2024-02-14 
• Deposition Author(s): Cheng, F., Xue, Y.P., Zheng, Y.G., Zou, S.P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.250 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Crystal Structure of phosphinothricin dehydrogenase

Cheng, F., Xue, Y.P., Zheng, Y.G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 280.86 kDa 
• Atom Count: 18,861 
• Modelled Residue Count: 2,378 
• Deposited Residue Count: 2,532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E [auth F], F [auth E]	422	Lysinibacillus composti	Mutation(s): 0  Gene Names: EBB45_13425
UniProt
Find proteins for A0A3N9UCW8 (Lysinibacillus composti) Explore A0A3N9UCW8  Go to UniProtKB:  A0A3N9UCW8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.250 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.13	α = 90
b = 126.667	β = 90
c = 223.741	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Cheng, F., Xue, Y.P., Zheng, Y.G., Zou, S.P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970046

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release