9JQS | pdb_00009jqs

Apo form of Oryza sativa solanesyl diphosphate synthase 3

PDB DOI: https://doi.org/10.2210/pdb9JQS/pdb

Classification: TRANSFERASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-28 Released: 2025-12-17
Deposition Author(s): Yang, G.-F., Xiao, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.260 (Depositor), 0.259 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.210 (Depositor)

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

Ligand Structure Quality Assessment

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

Literature

Apo form of Oryza sativa solanesyl diphosphate synthase 3

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

To be published.

Macromolecule Content

Total Structure Weight: 71.99 kDa
Atom Count: 5,028
Modeled Residue Count: 635
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable solanesyl-diphosphate synthase 3, chloroplastic	A, B	327	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: SPS3, Os12g0271700, LOC_Os12g17320, OsJ_1767i3 EC: 2.5.1.84
UniProt
Find proteins for Q0INZ4 (Oryza sativa subsp. japonica) Explore Q0INZ4 Go to UniProtKB: Q0INZ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0INZ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.260 (Depositor), 0.259 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.122	α = 90
b = 90.516	β = 90
c = 121.969	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

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: 2025-12-17
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.