8JPW

Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6

• PDB DOI: https://doi.org/10.2210/pdb8JPW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces sp. X-119-6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-13 Released: 2023-08-09 
• Deposition Author(s): Yamaguchi, H., Takahashi, K., Tatsumi, M., Tagami, U., Mizukoshi, T., Miyano, H., Sugiki, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.305 
• R-Value Work: 0.259 

Literature

Development of a novel single-chain l-glutamate oxidase from Streptomyces sp. X-119-6 by inserting flexible linkers

Yamaguchi, H., Takahashi, K., Tatsumi, M., Tagami, U., Mizukoshi, T., Miyano, H., Sugiki, M.

(2023) Enzyme Microb Technol 170: 110287

• DOI: https://doi.org/10.1016/j.enzmictec.2023.110287

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 74.37 kDa 
• Atom Count: 4,940 
• Modelled Residue Count: 594 
• Deposited Residue Count: 661 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-glutamate oxidase	A	661	Streptomyces sp. X-119-6	Mutation(s): 0  Gene Names: Lgox
UniProt
Find proteins for Q8L3C7 (Streptomyces sp) Explore Q8L3C7  Go to UniProtKB:  Q8L3C7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
AKG (Subject of Investigation/LOI)	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.305 
• R-Value Work: 0.259 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.4	α = 90
b = 158.4	β = 90
c = 138.235	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Yamaguchi, H., Takahashi, K., Tatsumi, M., Tagami, U., Mizukoshi, T., Miyano, H., Sugiki, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Refinement description