1TV3 | pdb_00001tv3

Crystal structure of the N-methyl-hydroxylamine MtmB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.168 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Reactivity and chemical synthesis of L-pyrrolysine- the 22(nd) genetically encoded amino acid

Hao, B.Zhao, G.Kang, P.T.Soares, J.A.Ferguson, T.K.Gallucci, J.Krzycki, J.A.Chan, M.K.

(2004) Chem Biol 11: 1317-1324

  • DOI: https://doi.org/10.1016/j.chembiol.2004.07.011
  • Primary Citation Related Structures: 
    1TV2, 1TV3, 1TV4

  • PubMed Abstract: 

    L-pyrrolysine, the 22(nd) genetically encoded amino acid, was previously deduced to be (4R, 5R)-4-substituted-pyrroline-5-carboxylate attached to the epsilon-nitrogen of lysine based on the crystal structure of the M. barkeri monomethylamine methyltransferase (MtmB). To confirm L-pyrrolysine's identity, structures of MtmB have been determined following treatment with hydroxylamine, N-methylhydroxylamine, or dithionite. Analysis of these structures has provided additional support for the presence of the pyrroline ring and, together with previous mass spectroscopy data, has led us to assign the C(4)-substituent to a methyl group. Based on this assignment, synthetic L-pyrrolysine was prepared by chemical methods. Detailed study of this chemically synthesized L-pyrrolysine has allowed us to characterize its physical properties, to study its chemical stability, and to elucidate the role of its C(4) substituent. Future applications of this synthetic L-pyrrolysine include its in vivo incorporation into recombinant proteins.


  • Organizational Affiliation
    • Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA.

Macromolecule Content 

  • Total Structure Weight: 50.36 kDa 
  • Atom Count: 4,004 
  • Modeled Residue Count: 457 
  • Deposited Residue Count: 458 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monomethylamine methyltransferase mtmB1458Methanosarcina barkeriMutation(s): 0 
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO30642
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BG4

Query on BG4



Download:Ideal Coordinates CCD File
B [auth A]5-(HYDROXY-METHYL-AMINO)-3-METHYL-PYRROLIDINE-2-CARBOXYLIC ACID
C7 H14 N2 O3
PGYJBAGGGAUHGV-HSUXUTPPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.168 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.987α = 90
b = 157.987β = 90
c = 136.914γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary