3K0B

Crystal structure of a predicted N6-adenine-specific DNA methylase from Listeria monocytogenes str. 4b F2365

• PDB DOI: https://doi.org/10.2210/pdb3K0B/pdb

• Classification: structural genomics, unknown function
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-24 Released: 2009-10-13 
• Deposition Author(s): Nocek, B., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal structure of a predicted N6-adenine-specific DNA methylase from Listeria monocytogenes str. 4b F2365

Nocek, B., Xu, X., Cui, H., Ng, J., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

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: 44.77 kDa 
• Atom Count: 3,532 
• Modelled Residue Count: 380 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
predicted N6-adenine-specific DNA methylase	A	393	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: LMOf2365_1916

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.949	α = 90
b = 46.156	β = 131.09
c = 91.376	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
DM	model building
ARP/wARP	model building
Coot	model building
CCP4	model building
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Nocek, B., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance