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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free:
0.270 (Depositor), 0.273 (DCC)
R-Value Work:
0.212 (Depositor), 0.225 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

serine hydroxymethyltransferase

Li, Z.R., Bai, L.Y.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8M0FGR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.270 (Depositor), 0.273 (DCC)
R-Value Work: 0.212 (Depositor), 0.225 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.