9JN6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.222 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1ECNClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMN-binding proteinA [auth B],
B [auth C],
C [auth D],
D [auth A]
218Kutzneria sp. 744Mutation(s): 1 
Gene Names: KUTG_08928
UniProt
Find proteins for A8CF72 (Kutzneria sp. (strain 744))
Explore A8CF72 
Go to UniProtKB:  A8CF72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8CF72
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth B],
G [auth C],
H [auth D],
J [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1ECN (Subject of Investigation/LOI)
Query on A1ECN

Download Ideal Coordinates CCD File 
F [auth B],
I [auth D],
K [auth A]
(3~{S})-1,2-diazinane-3-carboxylic acid
C5 H10 N2 O2
BZIBRGSBQKLEDC-BYPYZUCNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.222 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.878α = 90
b = 101.613β = 90
c = 111.155γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1ECNClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA0911400

Revision History  (Full details and data files)

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