4KYW

Restriction endonuclease DPNI in complex with two DNA molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 4KYW

Classification: HYDROLASE / DNA

Total Structure Weight: 42442.96


Macromolecule Entities
Molecule Chains Length Organism Details
Type-2 restriction enzyme DpnI A 257 Streptococcus pneumoniae EC#: 3.1.21.4 IUBMB
Mutation: R134N
Gene Name(s): dpnC SP_1850
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3' C, D, E, F 10 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
6MA
Query on 6MA
C, D, E, F DNA LINKING C11 H16 N5 O6 P A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.201
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 95.70 α = 90.00
b = 101.05 β = 90.00
c = 114.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-29
  • Released Date: 2014-06-04
  • Deposition author(s): Mierzejewska, K., Siwek, W., Czapinska, H., Skowronek, K., Bujnicki, J.M., Bochtler, M.

Revision History

  • Version 1_0: 2014-06-04

    Type: Initial release

  • Version 1_1: 2014-07-02

    Type: Database references

  • Version 1_2: 2014-07-09

    Type: Database references

  • Version 1_3: 2014-08-20

    Type: Database references