6EKR | pdb_00006ekr

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.264 (Depositor), 0.256 (DCC)
R-Value Work:
0.209 (Depositor), 0.201 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

Total Structure Weight: 36.86 kDa
Atom Count: 2,503
Modeled Residue Count: 303
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type ii site-specific deoxyribonuclease	A	312	Klebsiella pneumoniae	Mutation(s): 2 EC: 3.1.21.4
UniProt
Find proteins for Q93K38 (Klebsiella pneumoniae) Explore Q93K38 Go to UniProtKB: Q93K38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93K38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.256 (DCC)
R-Value Work: 0.209 (Depositor), 0.201 (DCC)
R-Value Observed: 0.215 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Tamulaitiene, G.

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

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.