1KIA | pdb_00001kia

Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate

• PDB DOI: https://doi.org/10.2210/pdb1KIA/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-12-02 Released: 2003-06-10 
• Deposition Author(s): Takusagawa, F., Huang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate

Takusagawa, F., Huang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 131.67 kDa 
• Atom Count: 8,999 
• Modeled Residue Count: 1,100 
• Deposited Residue Count: 1,168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine N-methyltransferase	A, B, C, D	292	Rattus norvegicus	Mutation(s): 0  EC: 2.1.1.20
UniProt
Find proteins for P13255 (Rattus norvegicus) Explore P13255  Go to UniProtKB:  P13255

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	F [auth A], H [auth B], J [auth C], L [auth D]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ACT	E [auth A], G [auth B], I [auth C], K [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.95	α = 90
b = 117.01	β = 90
c = 137.78	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Takusagawa, F., Huang, Y.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations