7E8R

EcoT38I restriction endonuclease

• PDB DOI: https://doi.org/10.2210/pdb7E8R/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Peduovirus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-02 Released: 2022-03-02 
• Deposition Author(s): Kita, K., Mikami, B.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structural analysis of EcoT38I restriction endonuclease

Kita, K., Mikami, B.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.87 kDa 
• Atom Count: 3,074 
• Modelled Residue Count: 346 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EcoT38I restriction endonuclease	A	351	Peduovirus P2	Mutation(s): 0  Gene Names: ecoT38IR
UniProt
Find proteins for Q83VS8 (Peduovirus P2) Explore Q83VS8  Go to UniProtKB:  Q83VS8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.159	α = 90
b = 53.159	β = 90
c = 250	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
PHENIX	refinement
XDS	data reduction
XDS	data scaling
RESOLVE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Kita, K., Mikami, B.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16380061

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release