9VGL | pdb_00009vgl

Ancestral L-tryptophan synthase beta-subunit 1

PDB DOI: https://doi.org/10.2210/pdb9VGL/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: 1.70 Å
R-Value Free:
0.225 (Depositor), 0.232 (DCC)
R-Value Work:
0.190 (Depositor), 0.199 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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: 176.72 kDa
Atom Count: 12,605
Modeled Residue Count: 1,556
Deposited Residue Count: 1,588
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral L-tryptophan synthase beta-subunit 1	A, B [auth D], C, D [auth B]	397	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B [auth D], C, D [auth B]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.225 (Depositor), 0.232 (DCC)
R-Value Work: 0.190 (Depositor), 0.199 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.529	α = 90
b = 91.661	β = 105.27
c = 105.181	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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	24K17828
Japan Society for the Promotion of Science (JSPS)	Japan	23K19283

Revision History (Full details and data files)

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

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.