4ESJ

RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 4ESJ

Classification: HYDROLASE / DNA

Total Structure Weight: 72723.17


Macromolecule Entities
Molecule Chains Length Organism Details
Type-2 restriction enzyme DpnI A, B 257 Streptococcus pneumoniae EC#: 3.1.21.4 IUBMB
Mutation: R134N
Gene Name(s): dpnC spr1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3') C, D, E, F 10 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

C, D UNKNOWN ATOM OR ION
X
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: 2.05 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.198
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 130.52 α = 90.00
b = 98.41 β = 112.21
c = 83.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-23
  • Released Date: 2012-06-13
  • Deposition author(s): Siwek, W., Czapinska, H., Bochtler, M., Bujnicki, J.M., Skowronek, K.

Revision History

  • Version 1_0: 2012-06-13

    Type: Initial release

  • Version 1_1: 2012-10-17

    Type: Database references