1U3E Dna Binding Protein Dna date Jul 21, 2004
title Dna Binding And Cleavage By The Hnh Homing Endonuclease I-Hm
authors B.W.Shen, M.Landthaler, D.A.Shub, B.L.Stoddard
compound source
Molecule: 36-Mer
Chain: A
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-D(Cptptpapcpgptpgpgpgpapaptptpg Apgpc)-3';
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Pgptptpapgpgpcptpcpaptptpapcp
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Hnh Homing Endonuclease
Chain: M
Engineered: Yes
Organism_scientific: Bacillus Phage Spo1
Organism_taxid: 10685
Gene: Bacteriophage Sp01
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codon+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkyb1
symmetry Space Group: I 2 2 2
R_factor 0.216 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.000 108.300 248.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.92 Å
ligand EDO, MN, SR, TRS enzyme
Gene
Ontology
ChainFunctionProcessComponent
M
  • nuclease activity
  • endonuclease activity


    • Primary referenceDNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI., Shen BW, Landthaler M, Shub DA, Stoddard BL, J Mol Biol 2004 Sep 3;342(1):43-56. PMID:15313606
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1u3e.pdb1.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 1U3E
  • CSU: Contacts of Structural Units for 1U3E
  • Likely Quarternary Molecular Structure file(s) for 1U3E
  • Structure Factors (179 Kb)
  • Retrieve 1U3E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U3E from S2C, [Save to disk]
  • Re-refined 1u3e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1U3E 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 1U3E
  • 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
  • 3D motif for 1U3E, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u3em1, region M:1-105 [Jmol] [rasmolscript] [script source]
        - Domain d1u3em2, region M:106-174 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1u3e_B] [1u3e_M] [1u3e_C] [1u3e_A] [1u3e]
  • SWISS-PROT database: [P34081]
  • Domain organization of [HMUI_BPSP1] by SWISSPFAM
  • Domains found in 1U3E: [HNHc] [IENR1 ] by SMART
    • Other resources with information on 1U3E
  • Community annotation for 1U3E 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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