4INE | pdb_00004ine

Crystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine

• PDB DOI: https://doi.org/10.2210/pdb4INE/pdb

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


• Deposited: 2013-01-04 Released: 2014-01-15 
• Deposition Author(s): Lukk, T., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine

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: 104.63 kDa 
• Atom Count: 8,171 
• Modeled Residue Count: 859 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PMT-2	A, B	454	Caenorhabditis elegans	Mutation(s): 0  Gene Names: pmt-2 EC: 2.1.1.103
UniProt
Find proteins for Q22993 (Caenorhabditis elegans) Explore Q22993  Go to UniProtKB:  Q22993

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
OPE	D [auth A], G [auth B]	PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER C2 H8 N O4 P SUHOOTKUPISOBE-UHFFFAOYSA-N
BME	E [auth A], H [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.131	α = 107.18
b = 68.011	β = 96.3
c = 74.742	γ = 106.51

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Lukk, T., Nair, S.K.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description