8ZGV | pdb_00008zgv

Drimenyl diphosphate synthase SsDMS_F248A&D303E from Streptomyces showdoensis in complex with farnesyl diphosphate (FPP) and Mg2+

• PDB DOI: https://doi.org/10.2210/pdb8ZGV/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces showdoensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-05-09 Released: 2025-05-21 
• Deposition Author(s): Pan, X.M., Dong, S.M., Dong, L.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Catalytic bases in class II terpene cyclases

Pan, X.M., Dong, S.M., Dong, L.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.97 kDa 
• Atom Count: 4,082 
• Modeled Residue Count: 471 
• Deposited Residue Count: 539 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Squalene cyclase C-terminal domain-containing protein	A	539	Streptomyces showdoensis	Mutation(s): 2  Gene Names: VO63_21045 EC: 5.4.99
UniProt
Find proteins for A0A2P2GK84 (Streptomyces showdoensis) Explore A0A2P2GK84  Go to UniProtKB:  A0A2P2GK84

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPP (Subject of Investigation/LOI)	B [auth A]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
MG (Subject of Investigation/LOI)	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.48	α = 90
b = 114.12	β = 90
c = 180.739	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Pan, X.M., Dong, S.M., Dong, L.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82073746

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release