9K0A | pdb_00009k0a

Structure of Pictet-Spenglerases KslB in complex with product

• PDB DOI: https://doi.org/10.2210/pdb9K0A/pdb

• Classification: LIGASE
• Organism(s): Kitasatospora
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-15 Released: 2025-06-18 
• Deposition Author(s): Mori, T., Renata, H., Abe, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: in silico

Literature

Structure of Pictet-Spenglerases KslB in complex with product

Mori, T., Renata, H., Abe, I.

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: 75.64 kDa 
• Atom Count: 4,844 
• Modeled Residue Count: 573 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cucumopine synthase C-terminal helical bundle domain-containing protein	A, B	337	Kitasatospora	Mutation(s): 0  Gene Names: KSE_70640
UniProt
Find proteins for E4NIM4 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054)) Explore E4NIM4  Go to UniProtKB:  E4NIM4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L46 (Subject of Investigation/LOI)	C [auth A], F [auth B]	(1~{S},3~{S})-1-(3-hydroxy-3-oxopropyl)-2,3,4,9-tetrahydropyrido[3,4-b]indole-1,3-dicarboxylic acid C16 H16 N2 O6 ZSFFNSLTDHOYOC-ZBEGNZNMSA-N
GOL	D [auth A], E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.077	α = 90
b = 82.992	β = 109.321
c = 64.501	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Mori, T., Renata, H., Abe, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release