7YLO

Conversion of indole-3-acetic acid into indole-3-aldehyde in bacteria Metabolic network of tryptophan around the indole-3-aldehyde formation

• PDB DOI: https://doi.org/10.2210/pdb7YLO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Limosilactobacillus fermentum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-26 Released: 2023-07-05 
• Deposition Author(s): Cheng, J., Luo, Y., Zhu, J., Tan, R., Wang, N., Lebedev, A.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 

Literature

Conversion of indole-3-acetic acid into indole-3-aldehyde in bacteria Metabolic network of tryptophan around the indole-3-aldehyde formation

Luo, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73.84 kDa 
• Atom Count: 5,302 
• Modelled Residue Count: 622 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyp-type peroxidase	A, B	313	Limosilactobacillus fermentum	Mutation(s): 0  Gene Names: BUW47_03110, C1Y38_03730, DBX48_02645, GC247_08580, GDZ34_00450, GJA14_02385, LACFE_CDS1279
UniProt
Find proteins for A0A0G9GI91 (Limosilactobacillus fermentum) Explore A0A0G9GI91  Go to UniProtKB:  A0A0G9GI91

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.179	α = 90
b = 135.179	β = 90
c = 83.979	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Cheng, J., Luo, Y., Zhu, J., Tan, R., Wang, N., Lebedev, A.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release