8KIH

PhmA, a type I diterpene synthase without NST/DTE motif

• PDB DOI: https://doi.org/10.2210/pdb8KIH/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Phoma
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-23 Released: 2023-10-04 
• Deposition Author(s): Zhang, B., Ge, H.M., Zhu, A., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Biosynthesis of Platelet Activating Factor Antagonist Phomactins Revealing a New Class of Type I Diterpene Synthase

Zhang, L., Zhang, B., Zhu, A., Liu, S.H., Wu, R., Zhang, X., Xu, Z.R., Ge, H.M.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 38 kDa 
• Atom Count: 2,571 
• Modelled Residue Count: 291 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
diterpene synthase, PhmA	A	332	Phoma	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FGG (Subject of Investigation/LOI)	B [auth A]	(2Z,6E,10E)-2-fluoro-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl trihydrogen diphosphate C20 H35 F O7 P2 NZHGLLPGXYKTDW-HAQLZSGTSA-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: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.549	α = 90
b = 106.549	β = 90
c = 55.36	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Zhang, B., Ge, H.M., Zhu, A., Zhang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277051, 22193071, 22107048, 22077062, 81991522, 81991524
Other government	China	BK20220123

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release