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)

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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

Literature

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

Dong, S., Liu, L., Zhang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

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

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
UniProt
Find proteins for A0A2U3EYQ2 (Enterobacter sp. CGMCC 5087) Explore A0A2U3EYQ2  Go to UniProtKB:  A0A2U3EYQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	C [auth A], E [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Dong, S., Liu, L., Zhang, H.

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

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release