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)

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
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

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

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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	3D Interactions
VB4 (Subject of Investigation/LOI) Query on VB4 Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.