9KKA | pdb_00009kka

Structure of the K193M mutant of transaminase PhnW from Vibrio vulnificus in complex with PLP and AEP

• PDB DOI: https://doi.org/10.2210/pdb9KKA/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio vulnificus NBRC 15645 = ATCC 27562
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-13 Released: 2025-11-19 
• Deposition Author(s): Ma, Q., Han, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.184 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structure of the K193M mutant of transaminase PhnW from Vibrio vulnificus in complex with PLP and AEP

Ma, Q., Han, M.

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)

Macromolecule Content 

• Total Structure Weight: 81.75 kDa 
• Atom Count: 6,047 
• Modeled Residue Count: 726 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminoethylphosphonate--pyruvate transaminase	A, B	369	Vibrio vulnificus NBRC 15645 = ATCC 27562	Mutation(s): 0  Gene Names: phnW, VVA0476 EC: 2.6.1.37

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
P7I (Subject of Investigation/LOI)	D [auth A], G [auth B]	(2-aminoethyl)phosphonic acid C2 H8 N O3 P QQVDJLLNRSOCEL-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.184 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.672	α = 90
b = 72.51	β = 93.49
c = 103.942	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Ma, Q., Han, M.

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

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release