4JK3 | pdb_00004jk3

PylD holoenzyme (SeMet)

• PDB DOI: https://doi.org/10.2210/pdb4JK3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanosarcina barkeri str. Fusaro
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-09 Released: 2013-06-12 
• Deposition Author(s): Quitterer, F., Beck, P., Bacher, A., Groll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD).

Quitterer, F., Beck, P., Bacher, A., Groll, M.

(2013) Angew Chem Int Ed Engl 52: 7033-7037

• PubMed: 23720358 
• DOI: https://doi.org/10.1002/anie.201301164
• Primary Citation Related Structures: 
  4J43, 4J49, 4J4B, 4J4H, 4JK3

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Organizational Affiliation: 
• Center for Integrated Protein Science Munich 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.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.74 kDa 
• Atom Count: 3,939 
• Modeled Residue Count: 502 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PylD	A, B	259	Methanosarcina barkeri str. Fusaro	Mutation(s): 0  Gene Names: Mbar_A0835 EC: 1.4.1
UniProt
Find proteins for Q46E80 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore Q46E80  Go to UniProtKB:  Q46E80

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.65	α = 90
b = 155.4	β = 90
c = 39.57	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Quitterer, F., Beck, P., Bacher, A., Groll, M.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary