8ZK6 | pdb_00008zk6

Crystal structure of the Decarboxylase KDC4427 from Enterobacter sp. CGMCC 5087

PDB DOI: https://doi.org/10.2210/pdb8ZK6/pdb

Classification: LYASE
Organism(s): Enterobacter sp. CGMCC 5087
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-15 Released: 2025-05-21
Deposition Author(s): Dong, S., Liu, L., Zhang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.208 (Depositor), 0.209 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Mechanistic Insights into the Substrate Promiscuity of alpha-Ketoacid Decarboxylases for Enhanced Higher-Alcohol Biosynthesis

Dong, S., Liu, L., Yang, Y., Liao, W., Zhang, X., Ling, C., Han, Y., Wang, L., Zhang, H.

(2026) ACS Sustain Chem Eng

DOI: https://doi.org/10.1021/acssuschemeng.5c13943

Macromolecule Content

Total Structure Weight: 124.81 kDa
Atom Count: 9,196
Modeled Residue Count: 1,076
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indolepyruvate decarboxylase	A, B	566	Enterobacter sp. CGMCC 5087	Mutation(s): 0 Gene Names: ipdC, DEO48_12930

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.224 (Depositor), 0.223 (DCC)
R-Value Work: 0.208 (Depositor), 0.209 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.23	α = 90
b = 170.29	β = 90
c = 115.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171203

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release
Version 1.1: 2026-05-20
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.