3LCC | pdb_00003lcc

Structure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb3LCC/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-10 Released: 2010-05-19 
• Deposition Author(s): Schmidberger, J.W., O'Hagan, D., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.177 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Halomethane Biosynthesis: Structure of a SAM-Dependent Halide Methyltransferase from Arabidopsis thaliana

Schmidberger, J.W., James, A.B., Edwards, R., Naismith, J.H., O'Hagan, D.

(2010) Angew Chem Int Ed Engl 49: 3646-3648

• PubMed: 20376845 
• DOI: https://doi.org/10.1002/anie.201000119
• Primary Citation Related Structures: 
  3LCC


• PubMed Abstract: 
  

  A product structure of the halomethane producing enzyme in plants ( Arabidopsis thaliana ) is reported and a model for presentation of chloride/bromide ion to the methyl group of S-adenosyl-L-methionine (SAM) is presented to rationalise nucleophilic halide attack for halomethane production, gaseous natural products that are produced globally.

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Organizational Affiliation: 
• University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST UK.

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: 26.81 kDa 
• Atom Count: 1,956 
• Modeled Residue Count: 216 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyl chloride transferase	A	235	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AtHOL1 EC: 2.1.1
UniProt
Find proteins for Q0WP12 (Arabidopsis thaliana) Explore Q0WP12  Go to UniProtKB:  Q0WP12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.177 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.43	α = 90
b = 54.43	β = 90
c = 263.5	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Schmidberger, J.W., O'Hagan, D., Naismith, J.H.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description