Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 50.29 kDa 
• Atom Count: 4100 
• Modelled Residue Count: 457 
• Deposited Residue Count: 458 
• Unique protein chains: 1

1NTH

Crystal structure of the methanosarcina barkeri monomethylamine methyltransferase (MTMB)

• PDB DOI: 10.2210/pdb1NTH/pdb
• Entry: 1NTH supersedes: 1L2R

• Classification: TRANSFERASE
• Organism(s): Methanosarcina barkeri
• Mutation(s): No 


• Deposited: 2003-01-30 Released: 2003-02-04 
• Deposition Author(s): Hao, B., Gong, W., Ferguson, T.K., James, C.M., Krzycki, J.A., Chan, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.188 
• R-Value Work: 0.176 

Literature

A new UAG-encoded residue in the structure of a methanogen methyltransferase

Hao, B., GONG, W., FERGUSON, T.K., JAMES, C.M., KRZYCKI, J.A., Chan, M.K.

(2002) Science 296: 1462-1466

• PubMed: 12029132 
• DOI: 10.1126/science.1069556
• Primary Citation of Related Structures:  
  1L2Q, 1NTH


• PubMed Abstract: 
  

Genes encoding methanogenic methylamine methyltransferases all contain an in-frame amber (UAG) codon that is read through during translation. We have identified the UAG-encoded residue in a 1.55 angstrom resolution structure of the Methanosarcina barkeri monomethylamine methyltransferase (MtmB). This structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold. The electron density for the UAG-encoded residue is distinct from any of the 21 natural amino acids. Instead it appears consistent with a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate. We suggest that this amino acid be named l-pyrrolysine.

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Organizational Affiliation: 

Department of Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monomethylamine methyltransferase mtmB1	A	458	Methanosarcina barkeri	Mutation(s): 0  Gene Names: mtmB1, mtmB EC: 2.1.1 (PDB Primary Data), 2.1.1.248 (UniProt)
UniProt
Find proteins for O30642 (Methanosarcina barkeri) Explore O30642  Go to UniProtKB:  O30642

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.188 
• R-Value Work: 0.176 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.464	α = 90
b = 158.464	β = 90
c = 135.797	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-30 
• Released Date: 2003-02-04 
Deposition Author(s): Hao, B., Gong, W., Ferguson, T.K., James, C.M., Krzycki, J.A., Chan, M.K.
• This entry supersedes: 1L2R

Revision History  

• Version 1.0: 2003-02-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-08-13
  Changes: Non-polymer description, Structure summary