4H0N | pdb_00004h0n

Crystal structure of Spodoptera frugiperda DNMT2 E260A/E261A/K263A mutant

• PDB DOI: https://doi.org/10.2210/pdb4H0N/pdb

• Classification: TRANSFERASE
• Organism(s): Spodoptera frugiperda
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-09-09 Released: 2012-11-14 
• Deposition Author(s): Li, S., Du, J., Yang, H., Yin, J., Zhong, J., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Functional and structural characterization of DNMT2 from Spodoptera frugiperda.

Li, S., Du, J., Yang, H., Yin, J., Ding, J., Zhong, J.

(2013) J Mol Cell Biol 5: 64-66

• PubMed: 23103599 
• DOI: https://doi.org/10.1093/jmcb/mjs057
• Primary Citation of Related Structures:  
  4H0N

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 155.51 kDa 
• Atom Count: 11,038 
• Modeled Residue Count: 1,324 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNMT2	A, B, C, D	333	Spodoptera frugiperda	Mutation(s): 3  Gene Names: DNMT2 EC: 2.1.1 (PDB Primary Data), 2.1.1.37 (UniProt), 2.1.1.204 (UniProt)
UniProt
Find proteins for A0A2H1VE33 (Spodoptera frugiperda) Explore A0A2H1VE33  Go to UniProtKB:  A0A2H1VE33

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], G [auth B], I [auth C], K [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CA	F [auth A], H [auth B], J [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.394	α = 90
b = 106.154	β = 90
c = 151.016	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Li, S., Du, J., Yang, H., Yin, J., Zhong, J., Ding, J.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description