3KO2 Hydrolase Dna date Nov 13, 2009
title I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c
authors G.K.Taylor, B.L.Stoddard
compound source
Molecule: Site-Specific Dna Endonuclease I-Msoi
Chain: A, B, F, G
Engineered: Yes
Mutation: Yes
Organism_scientific: Monomastix Sp.
Organism_taxid: 141716
Strain: Oke-1
Gene: I-Msoi, Orf170
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24d

Molecule: 5'-D(Gpcpapgpapcpcpgptpcpgptpgpapg Gptptpcpcpg)-3';
Chain: C, H
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: 5'-D(Cpgpgpapapcptpgptpcptpcpapcpg Gptpcptpgpc)-3';
Chain: D, I
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 1
R_factor 0.248 R_Free 0.286
length a length b length c angle alpha angle beta angle gamma
49.031 70.006 72.258 81.66 70.00 89.48
method X-Ray Diffractionresolution 2.90 Å
ligand CA enzyme
F, A, G, B
  • endonuclease activity

  • Primary referenceComputational reprogramming of homing endonuclease specificity at multiple adjacent base pairs., Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D, Nucleic Acids Res. 2010 Apr 30. PMID:20435674
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (3ko2.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (3ko2.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 3KO2
  • CSU: Contacts of Structural Units for 3KO2
  • Structure Factors (134 Kb)
  • Retrieve 3KO2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KO2 from S2C, [Save to disk]
  • Re-refined 3ko2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KO2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3KO2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3KO2, from MSDmotif at EBI
  • Fold representative 3ko2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ko2_F] [3ko2_H] [3ko2_B] [3ko2_C] [3ko2_A] [3ko2_I] [3ko2_G] [3ko2] [3ko2_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KO2
  • Community annotation for 3KO2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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