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.

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2H1VE33
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-14

Deposition Author(s):

Revision History (Full details and data files)

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

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 4H0N | pdb_00004h0n

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

Functional and structural characterization of DNMT2 from Spodoptera frugiperda.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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