8ZUW | pdb_00008zuw

Crystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb8ZUW/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-10 Released: 2025-06-11 
• Deposition Author(s): Liu, S., Yulu, W., Guoming, D., Boting, W., Xin, F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.234 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple motifs

Liu, S., Boting, W., Xin, F.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 330.25 kDa 
• Atom Count: 22,585 
• Modeled Residue Count: 2,754 
• Deposited Residue Count: 2,886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase	A, B, C, D, E, F	481	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: DW780_22950, GAN91_24535, GAO51_14925 EC: 4.1.1.15
UniProt
Find proteins for Q8A4M9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A4M9  Go to UniProtKB:  Q8A4M9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.234 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.228	α = 90
b = 124.897	β = 100.52
c = 109.622	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Liu, S., Yulu, W., Guoming, D., Boting, W., Xin, F.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release