1P8K

The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor

Structural Biology Knowledgebase: 1P8K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1P8K

Classification: HYDROLASE / DNA

Total Structure Weight: 48641.50


Macromolecule Entities
Molecule Chains Length Organism Details
Intron-encoded endonuclease I-AniI Z 254 Aspergillus nidulans EC#: 3.1 IUBMB
Mutation: I61R, M66M, M90M
Gene Name(s): I-AniI
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3' A 18 synthetic
5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3' B 13 synthetic
5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3' C 16 synthetic
5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3' D 15 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

B, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
Z L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.239
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.46 α = 90.00
b = 72.84 β = 108.21
c = 65.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-07
  • Released Date: 2004-01-20
  • Deposition author(s): Stoddard, B.L., Bolduc, J.M.

Revision History

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