9KK8 | pdb_00009kk8

Structure of the transaminase PhnW from Vibrio vulnificus in complex with PLP

• PDB DOI: https://doi.org/10.2210/pdb9KK8/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: 2.40 Å
• R-Value Free: 
  0.214 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: in silico

Literature

Structure of the transaminase PhnW from Vibrio vulnificus in complex with PLP

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.71 kDa 
• Atom Count: 2,826 
• Modeled Residue Count: 362 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.214 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.69	α = 90
b = 92.69	β = 90
c = 93.052	γ = 120

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