3FZ8

Crystal structure of glutamate decarboxylase beta from Escherichia coli: reduced Schiff base with PLP

• PDB DOI: https://doi.org/10.2210/pdb3FZ8/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-23 Released: 2009-02-03 
• Deposition Author(s): Malashkevich, V.N., De Biase, D., Bossa, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.165 
• R-Value Observed: 0.169 

Literature

Crystal structure of glutamate decarboxylase beta from Escherichia coli: reduced Schiff base with PLP

Malashkevich, V.N., De Biase, D., Bossa, 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)

Macromolecule Content

• Total Structure Weight: 317.77 kDa 
• Atom Count: 21,985 
• Modelled Residue Count: 2,747 
• Deposited Residue Count: 2,796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase beta	A, B, C, D, E, F	466	Escherichia coli K-12	Mutation(s): 0  Gene Names: b1493, gadB, JW1488 EC: 4.1.1.15
UniProt
Find proteins for P69910 (Escherichia coli (strain K12)) Explore P69910  Go to UniProtKB:  P69910

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLR	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE C8 H12 N O5 P RBCOYOYDYNXAFA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.165 
• R-Value Observed: 0.169 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.896	α = 90
b = 116.894	β = 90
c = 208.586	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Malashkevich, V.N., De Biase, D., Bossa, F.

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary