2VS7 Dna-Binding Protein date Apr 21, 2008
title The Crystal Structure Of I-Dmoi In Complex With Dna And Ca
authors M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya
compound source
Molecule: Homing Endonuclease I-Dmoi
Chain: A, D, G
Fragment: Residues 2-188
Synonym: I-Dmoi
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Desulfurococcus Mobilis
Organism_taxid: 2274
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosseta (De3) Plyss
Expression_system_vector: Pet24d

Molecule: 5'-D(Gpcpcptptpgpcpcpgpgp Gptpapapgptptpcpcpgpgpcpgpcpg)-3';
Chain: B, E, H

Synthetic: Yes
Organism_scientific: Desulfurococcus Mobilis
Organism_taxid: 2274

Molecule: 5'-D(Cpgpcpgpcpcpgpgpapap Cptptpapcpcpcpgpgpcpapapgpgpc)-3';
Chain: C, F, I

Synthetic: Yes
Organism_scientific: Desulfurococcus Mobilis
Organism_taxid: 2274
symmetry Space Group: P 1 21 1
R_factor 0.187 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.988 70.587 106.848 90.00 119.75 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand ACT, CA enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, G
  • nuclease activity
  • endonuclease activity


  • Primary referenceCrystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering., Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G, Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):16888-93. Epub 2008 Oct 30. PMID:18974222
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (337 Kb) [Save to disk]
  • Biological Unit Coordinates (2vs7.pdb1.gz) 111 Kb
  • Biological Unit Coordinates (2vs7.pdb2.gz) 114 Kb
  • Biological Unit Coordinates (2vs7.pdb3.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 2VS7
  • CSU: Contacts of Structural Units for 2VS7
  • Likely Quarternary Molecular Structure file(s) for 2VS7
  • Structure Factors (1132 Kb)
  • Retrieve 2VS7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VS7 from S2C, [Save to disk]
  • Re-refined 2vs7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VS7 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 2VS7
  • 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 2VS7, from MSDmotif at EBI
  • Fold representative 2vs7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vs7_A] [2vs7_C] [2vs7_D] [2vs7_B] [2vs7_F] [2vs7_H] [2vs7_G] [2vs7_I] [2vs7] [2vs7_E]
  • SWISS-PROT database: [P21505]
  • Domain organization of [DMO1_DESMO] by SWISSPFAM
  • Other resources with information on 2VS7
  • Community annotation for 2VS7 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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