6EKR

Crystal structure of Type IIP restriction endonuclease Kpn2I

• PDB DOI:  https://doi.org/10.2210/pdb6EKR/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-09-27 Released: 2018-10-10 
• Deposition Author(s): Tamulaitiene, G., Manakova, E., Grazulis, S., Siksnys, V.
• Funding Organization(s): Research Council of Lithuania, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 0.264 
• R-Value Work: 0.209 
• R-Value Observed: 0.215 

Literature

Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA

Tamulaitiene, G., Manakova, E., Jovaisaite, V., Grazulis, S., Siksnys, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
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: 36.81 kDa 
• Atom Count: 2,503 
• Modelled Residue Count: 303 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type ii site-specific deoxyribonuclease	A	312	Klebsiella pneumoniae	Mutation(s): 2  Gene Names: R EC: 3.1.21.4
UniProt
Find proteins for Q93K38 (Klebsiella pneumoniae) Explore Q93K38  Go to UniProtKB:  Q93K38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.88 Å
• R-Value Free: 0.264 
• R-Value Work: 0.209 
• R-Value Observed: 0.215 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.794	α = 90
b = 134.794	β = 90
c = 134.794	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Tamulaitiene, G., Manakova, E., Grazulis, S., Siksnys, V.

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Funding Organization	Location	Grant Number
Research Council of Lithuania	Lithuania	MIP-41/2013
European Union		BioStruct-X (grant agreement 283570)

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release