9VGK | pdb_00009vgk

Ancestral L-tryptophan synthase beta-subunit 1 complex with Trp-PLP

• PDB DOI: https://doi.org/10.2210/pdb9VGK/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-14 Released: 2025-11-12 
• Deposition Author(s): Ohata, M., Fujita, S., Uchida, K., Kobayashi, S., Chisuga, T., Nakano, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: in silico

Literature

Synthesis of L-Tryptophan Analogs by Ancestral L-Tryptophan Synthase beta-Subunit with High Organic Solvent Tolerance

Ohata, M., Fujita, S., Uchida, K., Kobayashi, S., Chisuga, T., Nakano, S.

(2025) ChemCatChem 

• DOI: https://doi.org/10.1002/cctc.202501027

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 177.31 kDa 
• Atom Count: 12,322 
• Modeled Residue Count: 1,556 
• Deposited Residue Count: 1,588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral L-tyrptophan synthase beta-subunit 1 K90A	A, B, C, D	397	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VB4 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan C19 H20 N3 O7 P MFRRQHVPLFTBMS-KCBMDGGTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.817	α = 90
b = 100.339	β = 90.34
c = 89.656	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Ohata, M., Fujita, S., Uchida, K., Kobayashi, S., Chisuga, T., Nakano, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23K19283
Japan Society for the Promotion of Science (JSPS)	Japan	24K17828

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release