9K99 | pdb_00009k99

Crystal structure of Setaria viridis SPS complexed with Aclonifen (surface polar residue mutant)

PDB DOI: https://doi.org/10.2210/pdb9K99/pdb

Classification: TRANSFERASE
Organism(s): Setaria viridis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-10-26 Released: 2026-04-29
Deposition Author(s): Xiao, H., Li, M., Yang, G.-F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.297 (Depositor), 0.296 (DCC)
R-Value Work:
0.242 (Depositor), 0.243 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Setaria viridis SPS complexed with Aclonifen (surface polar residue mutant)

Xiao, H., Li, M., Yang, G.-F.

To be published.

Macromolecule Content

Total Structure Weight: 142.08 kDa
Atom Count: 8,573
Modeled Residue Count: 1,117
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solanesyl diphosphate synthase	A, B, C, D	324	Setaria viridis	Mutation(s): 15 Gene Names: SEVIR_3G310000v2 EC: 2.5.1.84
UniProt
Find proteins for A0A4U6VI49 (Setaria viridis) Explore A0A4U6VI49 Go to UniProtKB: A0A4U6VI49
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4U6VI49
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L38 (Subject of Investigation/LOI) Query on A1L38 Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth C] MOL2 format, chain F [auth D] MOL2 format, chain E [auth C] mmCIF format, chain F [auth D] mmCIF format, chain E [auth C]	E [auth C], F [auth D]	Aclonifen C₁₂ H₉ Cl N₂ O₃ DDBMQDADIHOWIC-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.297 (Depositor), 0.296 (DCC)
R-Value Work: 0.242 (Depositor), 0.243 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.377	α = 104.95
b = 69.096	β = 112.43
c = 80.578	γ = 92.1

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-29

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-04-29
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.