1U3E

DNA binding and cleavage by the HNH homing endonuclease I-HmuI

Structural Biology Knowledgebase: 1U3E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1U3E

Classification: DNA binding protein / DNA

Total Structure Weight: 42874.38


Macromolecule Entities
Molecule Chains Length Organism Details
HNH homing endonuclease M 174 Bacillus virus spo1 Gene Name(s):
Macromolecule Entities
Molecule Chains Length Organism Details
36-MER A 36 synthetic
5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3' B 21 synthetic
5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3' C 15 synthetic

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

M 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SR
Query on SR

A, M STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C, M 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

M MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.216
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.00 α = 90.00
b = 108.30 β = 90.00
c = 248.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-07-21
  • Released Date: 2004-08-31
  • Deposition author(s): Shen, B.W., Landthaler, M., Shub, D.A., Stoddard, B.L.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4