9JN5 | pdb_00009jn5

Crystal structure of KtzT-C197A in complex with HEME and substrate

• PDB DOI: https://doi.org/10.2210/pdb9JN5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Kutzneria sp. 744
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-09-22 Released: 2025-01-29 
• Deposition Author(s): Li, Y.L., Yang, Y.Y., Huang, J.-W., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.302 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: in silico

Literature

Structural Insights into the N-N Bond-Formation Mechanism of the Heme-Dependent Piperazate Synthase KtzT

Yang, Y., Li, Y., Yao, L., Dai, K., Fu, X., Ge, A., Huang, J.W., Guo, R.T., Chen, C.C.

(2025) ACS Catal 15: 1265-1273

• DOI: https://doi.org/10.1021/acscatal.4c06124

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: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.76 kDa 
• Atom Count: 7,370 
• Modeled Residue Count: 849 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding protein	A, B, C, D	218	Kutzneria sp. 744	Mutation(s): 1  Gene Names: KUTG_08928
UniProt
Find proteins for A8CF72 (Kutzneria sp. (strain 744)) Explore A8CF72  Go to UniProtKB:  A8CF72

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], H [auth C], J [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ONH (Subject of Investigation/LOI)	F [auth A], I [auth C]	N~5~-hydroxy-L-ornithine C5 H12 N2 O3 OZMJDTPATROLQC-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.302 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.688	α = 90
b = 101.088	β = 90
c = 110.977	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Li, Y.L., Yang, Y.Y., Huang, J.-W., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA0911400

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release