3G5L

Crystal structure of putative S-adenosylmethionine dependent methyltransferase from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb3G5L/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-05 Released: 2009-02-17 
• Deposition Author(s): Patskovsky, Y., Sampathkumar, P., Gilmore, M., Miller, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal Structure of S-Adenosylmethionine Dependent Methyltransferase from Listeria Monocytogenes

Patskovsky, Y., Sampathkumar, P., Gilmore, M., Miller, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.87 kDa 
• Atom Count: 3,776 
• Modelled Residue Count: 435 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative S-adenosylmethionine dependent methyltransferase	A, B	253	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: LMOf2365_1325

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.812	α = 90
b = 92.532	β = 90
c = 99.973	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Patskovsky, Y., Sampathkumar, P., Gilmore, M., Miller, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references