9Y6B | pdb_00009y6b

CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE

PDB DOI: https://doi.org/10.2210/pdb9Y6B/pdb

Classification: TRANSFERASE
Organism(s): Glycine max
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-09-08 Released: 2026-04-08
Deposition Author(s): Beamer, L.J., Samarakoon, V., Owuocha, L.F.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.319 (Depositor), 0.320 (DCC)
R-Value Work:
0.282 (Depositor), 0.284 (DCC)
R-Value Observed:
0.284 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE

Beamer, L.J., Samarakoon, V., Owuocha, L.F.

To be published.

Macromolecule Content

Total Structure Weight: 272.27 kDa
Atom Count: 17,910
Modeled Residue Count: 2,299
Deposited Residue Count: 2,460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C, D, E	492	Glycine max	Mutation(s): 1 Gene Names: SHMT EC: 2.1.2.1
UniProt
Find proteins for K4FZF8 (Glycine max) Explore K4FZF8 Go to UniProtKB: K4FZF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K4FZF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLG (Subject of Investigation/LOI) Query on PLG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D] mmCIF format, chain J [auth E]	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C₁₀ H₁₅ N₂ O₇ P FEVQWBMNLWUBTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.319 (Depositor), 0.320 (DCC)
R-Value Work: 0.282 (Depositor), 0.284 (DCC)
R-Value Observed: 0.284 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.351	α = 90
b = 174.351	β = 90
c = 183.632	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	IOS 2152548

Revision History (Full details and data files)

Version 1.0: 2026-04-08
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.