Macromolecule Content

Total Structure Weight: 155.51 kDa
Atom Count: 11038
Residue Count: 1324
Unique protein chains: 1

4H0N

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

DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.256
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNMT2	A, B, C, D	333	Spodoptera frugiperda	Mutation(s): 3 Gene Names: DNMT2 EC: 2.1.1
Find proteins for L7MTK8 (Spodoptera frugiperda) Go to UniProtKB: L7MTK8
Protein Feature View Full Protein Feature View for L7MTK8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download CCD File	A, B, C, D	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Ligand Interaction
CA Query on CA Download CCD File	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.256
R-Value Work: 0.202
R-Value Observed: 0.204
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2012-09-09
Released Date: 2012-11-14

Deposition Author(s):

Revision History

Version 1.0: 2012-11-14
Type: Initial release
Version 1.1: 2013-02-27
Changes: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.