9SM5 | pdb_00009sm5

gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH and alpha-PSPP

• PDB DOI: https://doi.org/10.2210/pdb9SM5/pdb

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


• Deposited: 2025-09-05 Released: 2025-12-31 
• Deposition Author(s): Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.242 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural basis of methylation-triggered cyclization

Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 106.06 kDa 
• Atom Count: 6,670 
• Modeled Residue Count: 802 
• Deposited Residue Count: 915 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase domain protein	A, B, C	305	Pseudomonas chlororaphis	Mutation(s): 0  Gene Names: PchlO6_6042
UniProt
Find proteins for A0AB33WUZ9 (Pseudomonas chlororaphis O6) Explore A0AB33WUZ9  Go to UniProtKB:  A0AB33WUZ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JOQ	E [auth A]	alpha-presodorifen diphosphate C16 H30 O7 P2 ZODJECNQEXUGEC-WBUYXRLSSA-N
SAH (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4	G [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.242 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.45	α = 90
b = 83.67	β = 90.64
c = 121.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	GR 1861/13-1

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release