7E13 | pdb_00007e13

Caprylic acid targets a serine hydroxymethyltransferase to kill horseweed

• PDB DOI: https://doi.org/10.2210/pdb7E13/pdb

• Classification: PLANT PROTEIN
• Organism(s): Erigeron canadensis
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2021-01-29 Released: 2022-02-02 
• Deposition Author(s): Bai, L.Y., Li, Z.R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

serine hydroxymethyltransferase

Li, Z.R., Bai, L.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 229.03 kDa 
• Atom Count: 14,952 
• Modeled Residue Count: 1,900 
• Deposited Residue Count: 2,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
serine hydroxymethyltransferase	A, B, C, D	513	Erigeron canadensis	Mutation(s): 0  EC: 2.1.2.1
UniProt
Find proteins for A0A8M0FGR5 (Erigeron canadensis) Explore A0A8M0FGR5  Go to UniProtKB:  A0A8M0FGR5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.868	α = 90
b = 121.868	β = 90
c = 306.401	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Bai, L.Y., Li, Z.R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31801754

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description