3T7V

Crystal structure of methylornithine synthase (PylB)

• PDB DOI: https://doi.org/10.2210/pdb3T7V/pdb

• Classification: TRANSFERASE
• Organism(s): Methanosarcina barkeri str. Fusaro
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-31 Released: 2011-11-30 
• Deposition Author(s): Quitterer, F., List, A., Eisenreich, W., Bacher, A., Groll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.165 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 

Literature

Crystal structure of methylornithine synthase (PylB): insights into the pyrrolysine biosynthesis.

Quitterer, F., List, A., Eisenreich, W., Bacher, A., Groll, M.

(2012) Angew Chem Int Ed Engl 51: 1339-1342

• PubMed: 22095926 
• DOI: https://doi.org/10.1002/anie.201106765
• Primary Citation of Related Structures:  
  3T7V

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Organizational Affiliation: 

Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.

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: 40.95 kDa 
• Atom Count: 3,063 
• Modelled Residue Count: 337 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methylornithine synthase PylB	A	350	Methanosarcina barkeri str. Fusaro	Mutation(s): 0  Gene Names: Mbar_A0838 EC: 2.8.1.6 (PDB Primary Data), 5.4.99.58 (UniProt)
UniProt
Find proteins for Q46E78 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore Q46E78  Go to UniProtKB:  Q46E78

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MD0	D [auth A]	5-amino-D-isoleucine C6 H14 N2 O2 HYUPFEBCCJWDJX-RFZPGFLSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.165 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.02	α = 90
b = 77.02	β = 90
c = 104.95	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-30 
Deposition Author(s): Quitterer, F., List, A., Eisenreich, W., Bacher, A., Groll, M.

Revision History  

• Version 1.0: 2011-11-30
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations