9JZF | pdb_00009jzf

Crystal structure of OsSPS3 complexed with zoledronate and isopentenyl diphosphate

• PDB DOI: https://doi.org/10.2210/pdb9JZF/pdb

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


• Deposited: 2024-10-14 Released: 2025-12-17 
• Deposition Author(s): Xiao, H., Li, M., Yang, G.-F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.318 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of OsSPS3 complexed with zoledronate and isopentenyl diphosphate

Xiao, H., Li, M., Yang, G.-F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.77 kDa 
• Atom Count: 4,660 
• Modeled Residue Count: 607 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable solanesyl-diphosphate synthase 3, chloroplastic	A, B	324	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZOL	D [auth A]	ZOLEDRONIC ACID C5 H10 N2 O7 P2 XRASPMIURGNCCH-UHFFFAOYSA-N
IPE (Subject of Investigation/LOI)	C [auth A]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.318 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.048	α = 90
b = 90.718	β = 90
c = 125.568	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Xiao, H., Li, M., Yang, G.-F.

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

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release