4UT0 Hydrolase Dna date Jul 17, 2014
title The Crystal Structure Of I-Dmoi In Complex With Its Target Dna At 10 Days Incubation In 5mm Mn (State 7)
authors R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J. G.Montoya
compound source
Molecule: Homing Endonuclease I-Dmoi
Chain: A, F, K
Synonym: I-Dmoi
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Desulfurococcus Mobilis
Organism_taxid: 2274
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet24d

Molecule: 5'-D(Gpcpcptptpgpcpcpgpgpgptpapap)-
Chain: B, G, L

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Cpgpcpgpcpcpgpgpapapcptptpapc
Chain: D, I, N

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Gptptpcpcpgpgpcpgpcpgp)-3'
Chain: C, H, M

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Cpcpgpgpcpapapgpgpcp)-3'
Chain: E, J, O

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.1829 R_Free 0.2282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.984 70.387 107.154 90.00 119.81 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ACT, MN enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, K
  • nuclease activity
  • endonuclease activity


  • Primary referenceVisualizing phosphodiester-bond hydrolysis by an endonuclease., Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G, Nat Struct Mol Biol. 2014 Dec 8. doi: 10.1038/nsmb.2932. PMID:25486305
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (4ut0.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (4ut0.pdb2.gz) 55 Kb
  • Biological Unit Coordinates (4ut0.pdb3.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 4UT0
  • CSU: Contacts of Structural Units for 4UT0
  • Structure Factors (2946 Kb)
  • Retrieve 4UT0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UT0 from S2C, [Save to disk]
  • Re-refined 4ut0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UT0 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 4UT0
  • 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 4UT0, from MSDmotif at EBI
  • Fold representative 4ut0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ut0_C] [4ut0_M] [4ut0_A] [4ut0_K] [4ut0_G] [4ut0_F] [4ut0_E] [4ut0_N] [4ut0_B] [4ut0_D] [4ut0_I] [4ut0_J] [4ut0_H] [4ut0] [4ut0_L] [4ut0_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4UT0
  • Community annotation for 4UT0 at PDBWiki (http://pdbwiki.org)

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