4IV8 | pdb_00004iv8

Crystal structure of N-methyl transferase from Plasmodium knowlesi complexed with S-adenosyl methionine

• PDB DOI: https://doi.org/10.2210/pdb4IV8/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium knowlesi strain H
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-22 Released: 2014-02-19 
• Deposition Author(s): Lukk, T., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.271 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Phosphoethanolamine N-methyl transferase is a Malarial drug target.

Lukk, T., Nair, S.K.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 67.33 kDa 
• Atom Count: 4,487 
• Modeled Residue Count: 490 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine N-methyltransferase,putative	A, B	284	Plasmodium knowlesi strain H	Mutation(s): 0  Gene Names: PKH_121150 EC: 2.1.1.103
UniProt
Find proteins for A0A384KJX3 (Plasmodium knowlesi (strain H)) Explore A0A384KJX3  Go to UniProtKB:  A0A384KJX3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], E [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
BME	D [auth A], F [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.71	α = 90
b = 96.76	β = 90
c = 38.46	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Lukk, T., Nair, S.K.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description