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), 0.237 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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), 0.237 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.