Download MendeleyStructural 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
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
- Funding Organization(s): Ministry of Science and Technology (MoST, China)
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
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| FMN-binding protein | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A8CF72 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on 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) Query on ONH | 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 Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data scaling |
| HKL-2000 | data reduction |
| PHASER | phasing |
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.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Science and Technology (MoST, China) | China | 2021YFA0911400 |
Revision History (Full details and data files)
- Version 1.0: 2025-01-29
Type: Initial release
