5E5S Hydrolase Dna date Oct 09, 2015
title I-Smami K103a Mutant
authors B.W.Shen
compound source
Molecule: I-Smami Laglidadg Meganuclease
Chain: A
Fragment: Unp Residues 114-415
Engineered: Yes
Mutation: Yes
Organism_scientific: Sordaria Macrospora (Strain Atcc Mya-3 997 K(L3346) K-Hell);
Organism_taxid: 771870
Strain: Atcc Mya-333 Dsm 997 K(L3346) K-Hell
Gene: Smac_12671
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Ril+
Expression_system_plasmid: Pet21d(+)

Molecule: Bottom Strand Dna
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Top Strand Dna Left Site
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pcpapgpgptpgptpapcpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.251
length a length b length c angle alpha angle beta angle gamma
59.589 68.199 97.652 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.29 Å
ligand MG, PG0 enzyme

Primary referenceThe Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease., Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK, J Mol Biol. 2015 Dec 15. pii: S0022-2836(15)00696-8. doi:, 10.1016/j.jmb.2015.12.005. PMID:26705195
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (5e5s.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5E5S
  • CSU: Contacts of Structural Units for 5E5S
  • Structure Factors (334 Kb)
  • Retrieve 5E5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E5S from S2C, [Save to disk]
  • Re-refined 5e5s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E5S 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 5E5S
  • 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
  • Fold representative 5e5s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e5s] [5e5s_D] [5e5s_B] [5e5s_C] [5e5s_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5E5S
  • Community annotation for 5E5S at PDBWiki (http://pdbwiki.org)

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