7ZKH

C-Methyltransferase PsmD from Streptomyces griseofuscus with bound cofactor (crystal form 1)

• PDB DOI: https://doi.org/10.2210/pdb7ZKH/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces griseofuscus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-04-13 Released: 2022-12-28 
• Deposition Author(s): Weiergraeber, O.H., Amariei, D.A., Pozhydaieva, N., Pietruszka, J.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.185 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD-Crystal Structure, Catalytic Mechanism, and Preparative Applications

Amariei, D.A., Pozhydaieva, N., David, B., Schneider, P., Classen, T., Gohlke, H., Weiergraber, O.H., Pietruszka, J.

(2022) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.2c04240

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 31.31 kDa 
• Atom Count: 2,649 
• Modelled Residue Count: 266 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A	275	Streptomyces griseofuscus	Mutation(s): 0  Gene Names: psmD
UniProt
Find proteins for W8R3D8 (Streptomyces griseofuscus) Explore W8R3D8  Go to UniProtKB:  W8R3D8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
UNL	B [auth A]	Unknown ligand ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.185 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.19	α = 90
b = 95.99	β = 90
c = 40.38	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Weiergraeber, O.H., Amariei, D.A., Pozhydaieva, N., Pietruszka, J.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description