7YLO | pdb_00007ylo

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular Insights into the One-Carbon Loss Oxidation of Indole-3-acetic Acid

Cheng, J., Wang, N., Yu, L., Luo, Y., Liu, A.K., Tang, S., Xu, J.Y., Wang, Y.S., Zhu, J., Lebedev, A., Tian, C.L., Tan, R.X.

(2024) ACS Catal 14: 8528-8540

DOI: https://doi.org/10.1021/acscatal.4c02178

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 EC: 1.11.1
UniProt
Find proteins for A0A0G9GI91 (Limosilactobacillus fermentum) Explore A0A0G9GI91 Go to UniProtKB: A0A0G9GI91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0G9GI91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.240 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
Version 1.2: 2025-01-22
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.